The Doctor encounters the Matrix.

[The Romulan Republic]

A simple scenario:

The 12th. Doctor and TARDIS, immediately following the most recent episode of Doctor Who, materialize in the hold of the Nebuchadnezzar, at the start of the first film in the Matrix trilogy.

How will the Doctor react? Will he be able free humanity? Will he achieve a peace between humans and machines, or will he simply destroy the Matrix's machine overlords?

Alternate scenario:

As above, but replace 12 with 11, Amy, and Rory.

And yes, I am aware of the obvious objection that the Doctor won't have the plug in the back of his neck to plug into the Matrix itself. But frankly, the Doctor operates on a whole different level technologically, so I'm prepared to be that he could tinker up a way for him and his companions to enter the Matrix if he cared to.

[mr friendly guy]

If you want a canon way for the Doctor to operate the Matrix, he managed to somehow connect to a futuristic human weapon system in the classic story "Warriors of the Deep." Generally the human operator was specially selected, had implants to allow them to interface with the system which makes it harder for enemies to hack. But not impossible if you're Silurians. Apparently the Doctor just connected himself in, because... Time Lord stuff. So I am prepared to buy that he could connect to the Matrix.

To answer the OP, I can only speculate that he could come up with a deal for the machines. Since the machines "motivations" as it were for keeping humans are
a. power source because... yeah lets not think about that too much and

b. Because humans might destroy them

He could potentially offer the machines another world (since they most probably don't have the same attachments to a homeland like humans), and in return gives them some super dooper power source so they don't need humans. There is precedence for the Doctor doing so even though it violates Time Lord rules in the classic episode "Planet of evil." Now that the Time Lords are out the way....

It depends on whether the machines will "trust" the Doctor to do so, and maybe he needs demonstrate such strategic and technological superiority and NOT destroy the machines, that they think the Doctor could be trusted to do a deal.

[FaxModem1]

12th Doctor?

Doctor: Humanity is enslaved by their machines and being used as a power supply? Not my problem. Clara, I'm leaving you here for a couple days. I'll be back after you've almost died 5 times.

The 11th Doctor?

He might rewire the entire Matrix with perception filters or some other gadget to wake them all up.

[Elheru Aran]

Just to clarify... 11th is Matt Smith, 12th is Capaldi?

I haven't watched much (or any really) of 11 and 12. I've watched mostly 9 and 10 (Tennant and Eccleston, bless his bald heart). Eccleston would quite possibly view the Machines as little better than the Daleks. That particular incarnation was a walking, talking case study of PTSD... Tennant would be a little more fascinated by the whole situation, but in some ways he would be as deadly as Eccleston could be.

[bilateralrope]

He could potentially offer the machines another world (since they most probably don't have the same attachments to a homeland like humans), and in return gives them some super dooper power source so they don't need humans.

From what I remember, the machines used to use solar power until the humans fucked with the sky to block all the sunlight. So a new planet would solve the machines power problems. So would nuclear power.

But the humans left behind on Earth are fucked due to the lack of an ecosystem to support them.

[NecronLord]

Why would he need to? The Doctor generally knows a bit about the history of where he is, why not just get back in the TARDIS and leave?

The ending of the Matrix series - peace and reconciliation between man and machine - is already pretty much optimal. Short of a few casualties in battle, it's hard to imagine how to improve the outcome.

[The Romulan Republic]

Why would he need to? The Doctor generally knows a bit about the history of where he is, why not just get back in the TARDIS and leave?

The ending of the Matrix series - peace and reconciliation between man and machine - is already pretty much optimal. Short of a few casualties in battle, it's hard to imagine how to improve the outcome.

That's a fair point, but...

The Doctor is not exactly one for just minding his own business. He'd probably stick around for a while just for the hell of it. Eleven would, anyway. Twelve might just be too grumpy to bother.

Also, how much he seems to know about historical events seems to vary. He certainly doesn't have 100% accurate foreknowledge of everything that happens on the series. And this is a franchise where history can be casually rewritten to an extent.

As to weather he could lead to a better outcome, the Doctor is great at solving an immediate crisis, but not too reliable when it comes to sticking around and cleaning up the aftermath. He swoops in, saves the day, and then moves on. He could probably end the war in one Matrix film instead of three (to the great relief of everyone who hated the sequels ). But I don't know weather the society that grew out of that after the war was over would be any better, except insofar as it would have more survivors.

[The Romulan Republic]

He could potentially offer the machines another world (since they most probably don't have the same attachments to a homeland like humans), and in return gives them some super dooper power source so they don't need humans.

From what I remember, the machines used to use solar power until the humans fucked with the sky to block all the sunlight. So a new planet would solve the machines power problems. So would nuclear power.

But the humans left behind on Earth are fucked due to the lack of an ecosystem to support them.

I wonder if this is something the Doctor could help with- de-scorching the sky? He'd certainly try, partly on general principle and partly because he's been to future eras where the sky was not infested with a nano-bot death swarm, so he'd know it wasn't supposed to remain that way and that if it did something was wrong with the timeline.

And if all else fails, yes, he could help relocate the population of Earth to another world. Or call in extra-terrestrial aid to do so.

[NecronLord]

What makes us think there would be more survivors? The Doctor has failed and failed tragically before. He might find some shutdown command that kills 20% of people in the matrix or something.

Of course the real answer is as per most Dr Who crossovers is that as per most crossovers, character shields shut down. He gets beaten up and imprisoned by the Neb's crew and then turned into sentinel chow at some point.

[NecronLord]

I wonder if this is something the Doctor could help with- de-scorching the sky? He'd certainly try, partly on general principle and partly because he's been to future eras where the sky was not infested with a nano-bot death swarm, so he'd know it wasn't supposed to remain that way and that if it did something was wrong with the timeline.

He also did nothing to about the Earth being wholly abandoned for a while and Earth becoming toxic in the Dr Who canon.



There's no reason to think he'd flip out about a disaster on Earth wiping out most of the surface - such things are only temporary.

[Elheru Aran]

Yeah... honestly the Doctor's reaction to Big Events (TM) to Earth in alternate timelines really varies a lot, from what I understand. Some incarnations are very concerned about it, some don't care. Obviously, the out-of-universe reason is that it's because of all the different actors, writers, and productions the character has gone through. In universe, it's simpler to say that we as viewers are going to have issues predicting what the Doctor will do, because he's a.) fallible and b.) not actually human himself. There have been a good number of incidents where he only intervenes because his companions ask him to or get into trouble themselves.

[The Romulan Republic]

What makes us think there would be more survivors? The Doctor has failed and failed tragically before. He might find some shutdown command that kills 20% of people in the matrix or something.

The Doctor's successes outweigh his failures by a wide margin, but he's certainly capable of failure, yes.

Still, I think that on the whole, he'd more likely make the situation better, not worse.

Of course the real answer is as per most Dr Who crossovers is that as per most crossovers, character shields shut down. He gets beaten up and imprisoned by the Neb's crew and then turned into sentinel chow at some point.

Yes, I think he'd get locked up initially. The Nebuchadnezzar is a warship, effectively, on which he will be (inadvertently) trespassing. But he just might be able to bluff with the psychic paper as well, although its not infallible.

If not, Morpheus likely goes to talk to the Oracle about him, at least once he realizes he's dealing with an alien (previously unknown, to my knowledge, in the Matrix-verse). I have no idea what the Oracle would tell him to do, or what she could tell him since its my understanding (I've only watched bits of the sequels) that she's not actually psychic but a program, so unless she has access to records of the Doctor's past involvement with Earth (possible), he's an outside context problem for her. And what she says probably determines how Morpheus proceeds regarding the Doctor, since he's a true believer.

Sentinel chow, though... the Sentinels aren't that big a threat when you get down to it, unless the Doctor decides to go hiking through the ruins (and even then the sonic screwdriver can fuck with machinery in any number of ways). Most likely, most of the time he'll be in either the Matrix (no sentinels, but more than made up for by the presence of Agents), on the Nebuchadnezzar (in which case he'll be protected by the ship's defences barring the crew simply chucking him overboard, and I doubt Morpheus would do that without cause), in the TARDIS (Hell will freeze over before a sentinel breaches the TARDIS's shields), or in Zion (in which case he'll be behind the defences of Zion, for whatever they're worth).

Give the Doc some credit- he's survived much worse than flying metal octopi, character shields or no.

[FaxModem1]

The sentinels don't take prisoners or give speeches, two things that all of the Doctor's enemies do that he usually exploits. As for his sonic screwdriver saving the day, that would really depend on him being able to make EMPs with it. Something that, as shown in 'Voyage of the Damned' against the robot angels, he and the passengers needed the cybernetic power source of an alien cyborg in order to fight them at all. Has the Doctor ever demonstrated the ability to make EMPs with his screwdriver?

His only hope is that the sentinels determine he's alien enough to warrant investigation and bring him before the sentinel baby face to talk it to death.

[The Romulan Republic]

The sentinels don't take prisoners or give speeches, two things that all of the Doctor's enemies do that he usually exploits. As for his sonic screwdriver saving the day, that would really depend on him being able to make EMPs with it. Something that, as shown in 'Voyage of the Damned' against the robot angels, he and the passengers needed the cybernetic power source of an alien cyborg in order to fight them at all. Has the Doctor ever demonstrated the ability to make EMPs with his screwdriver?

I seem to recall him using it to disable Silurian guns in "The Hungry Earth"/"Cold Blood", though its been a long time since I watched that story. That was Eleven, by the way.

But there are other options. Eleven also used it as an outright energy weapon against the Silence in "Day of the Moon" (granted, a Silence probably takes less firepower to take out than a sentinel) and I think he used it to create a shield or forcefield on at least one occasion (might have been "Rings of Ankhaten").

Honestly, the sonic screwdriver seems to do whatever the writer wants it to do today, for the most part.

His only hope is that the sentinels determine he's alien enough to warrant investigation and bring him before the sentinel baby face to talk it to death.

Possible.

But in any case, again, its likely a moot point unless he's walking through the ruins or the sentinels manage to overwhelm the defences of the Nebuchadnezzar or wherever else the Doctor ends up.

[FaxModem1]

The sentinels don't take prisoners or give speeches, two things that all of the Doctor's enemies do that he usually exploits. As for his sonic screwdriver saving the day, that would really depend on him being able to make EMPs with it. Something that, as shown in 'Voyage of the Damned' against the robot angels, he and the passengers needed the cybernetic power source of an alien cyborg in order to fight them at all. Has the Doctor ever demonstrated the ability to make EMPs with his screwdriver?

I seem to recall him using it to disable Silurian guns in "The Hungry Earth"/"Cold Blood", though its been a long time since I watched that story. That was Eleven, by the way.

But there are other options. Eleven also used it as an outright energy weapon against the Silence in "Day of the Moon" (granted, a Silence probably takes less firepower to take out than a sentinel) and I think he used it to create a shield or forcefield on at least one occasion (might have been "Rings of Ankhaten").

Honestly, the sonic screwdriver seems to do whatever the writer wants it to do today, for the most part.

And yet the Doctor is in living fear of handguns wielded by American Secret Service agents. No forcefields or disabling of weapons there. So, maybe Silurian weapons are just crap?

[The Romulan Republic]

The sentinels don't take prisoners or give speeches, two things that all of the Doctor's enemies do that he usually exploits. As for his sonic screwdriver saving the day, that would really depend on him being able to make EMPs with it. Something that, as shown in 'Voyage of the Damned' against the robot angels, he and the passengers needed the cybernetic power source of an alien cyborg in order to fight them at all. Has the Doctor ever demonstrated the ability to make EMPs with his screwdriver?

I seem to recall him using it to disable Silurian guns in "The Hungry Earth"/"Cold Blood", though its been a long time since I watched that story. That was Eleven, by the way.

But there are other options. Eleven also used it as an outright energy weapon against the Silence in "Day of the Moon" (granted, a Silence probably takes less firepower to take out than a sentinel) and I think he used it to create a shield or forcefield on at least one occasion (might have been "Rings of Ankhaten").

Honestly, the sonic screwdriver seems to do whatever the writer wants it to do today, for the most part.

And yet the Doctor is in living fear of handguns wielded by American Secret Service agents. No forcefields or disabling of weapons there. So, maybe Silurian weapons are just crap?

My guess would be that the sonic screwdriver can screw up high tech. weaponry but is less effective against a more simple mechanical device.

That or he simply didn't have it out and ready to go when the Secret Service caught him (I don't recall), and didn't want to trust his ability to activate it faster than a Secret Service agent could pull a trigger.

Also, sentinels are kind of shit too. No substantial ranged weapons to the best of my recollections. They have to be right on top of a ship to attack it.

Edit: Although that raises another interesting question- what is the range limit on a sonic screwdriver?

[FaxModem1]

My guess would be that the sonic screwdriver can screw up high tech. weaponry but is less effective against a more simple mechanical device.

That or he simply didn't have it out and ready to go when the Secret Service caught him (I don't recall), and didn't want to trust his ability to activate it faster than a Secret Service agent could pull a trigger.

Also, sentinels are kind of shit too. No substantial ranged weapons to the best of my recollections. They have to be right on top of a ship to attack it.

Edit: Although that raises another interesting question- what is the range limit on a sonic screwdriver?

Well, aside from the Silurians, has the Doctor disabled other weapons with the sonic screwdriver? I don't remember him ever doing so against a Cyberman's weapons, or a Dalek's, a Sontaran, etc.

If he has, great, then in the words of Scotty, "The more they overthink the plumbing, the easier it is to stop up the drain."

If not, maybe Silurian weapons are just crap.

[The Romulan Republic]

The only example of the Doctor taking out a Dalek with the sonic screwdriver I can think of is when three different versions of the Doctor combined their sonic screwdrivers to literally blast a Dalek into another reality, destroying it in the process. This was in Day of the Doctor. Obviously not a typical example, both because of the presence of multiple Doctors and because I'd speculate that the War Doctor's screwdriver would likely have been a more weaponized model.

Cybermen/Sontarans/etc., I'm not sure.

[NecronLord]

The sentinels lacking ranged weapons seems to be a feature, not a bug; they're designed to pose a challenge without being overwhelming, as the Architect reveals in the sequels, the machines knew where Zion was all along and could have attacked at any time.

Sentinels are dangerous, and lethal, but they're not really intended to wipe humans out, merely challenge them and keep them busy.

When Neo and Trinity go to Zero One, we see that the artillery machines there are much better armed.

As for operating in the Matrix, well we happen to have basically seen that in the series, as the Time Lords have one on Gallifrey.



Given that the Valeyard is ostensibly a (alternate?) regeneration of the Doctor between the 12th and final (which makes more sense as a phrase now that the doctor has another regeneration cycle) 12's power in the matrix might be more like him, with easy teleportation and the ability to create structures as he wishes.

Certainly it's clear that the Valeyard's better at operating in the Matrix than the 6th Doctor, who is better at it than the 4th.

None of the three doctor regenerations show there is as kinetic or kung-fu as the likes of Agents and so forth, but then, the Valeyard might not need to be, he could possibly just blink away from attacks.

I still think the best thing the Doctor can do in this scenario is to follow the old Time Lord proverb; Do Nothing, and All will be Well. He's probably smart enough to figure out that the machines don't really want to wipe out humanity, particularly if he gets access to the Zion Archive (As per the Animatrix, Second Renaissance) at any point.

If he really wants to be helpful, he would be most useful coming back twenty years later and helping with the sky problem.



I expect he knows how to build one of those.

[The Romulan Republic]

Do the machines have any forces outside of the Matrix besides sentinels (flying shit as far as serious combat is concerned) and the artillery you mentioned?

I can't imagine the artillery being a big issue for the Doctor. Even if he did decide to venture within its range, artillery isn't generally intended to take out lone infiltrators, and in any case he'd likely approach aboard the TARDIS, which has some fairly impressive shielding.

A lone sentinel might or might not be able to take him. Against a sentinel swarm... he'd likely be as vulnerable as anyone else I imagine, unless the sonic screwdriver can be effective at much greater ranges than I recall or he's had time to prepare some sort of defence.

As to how he'd fair in the Matrix, the point about the Valeyard is interesting, and not something I was aware of (I've never seen those episodes). However, I must point out that the way the Matrix operates seems to be less about innate ability and more about state of mind. In other words, presuming he can function in the Matrix like a human can at all (differences in Time Lord brains, after all), the Doctor ought to be able to manipulate the Matrix in the same ways that Neo and company do if he believes that he can, if he accepts that its not real, just computer code.

In that, I think he might actually have leg up on them. Maybe not on Neo, who's a one off anomaly, but on ordinary human rebels who have been freed from the Matrix. After all, the Doctor is accustomed to dealing with the strange, with things being not as they seem, and has that Time Lord mind to work with. Shaping reality with his thoughts is likely to be a concept that comes much more readily to him than the average human.

Edit: Although punching, kicking, and shooting generally isn't his style. I'd be interested to see how the Doctor would bend reality in the Matrix, because I dare say he'd try for something a bit more creative.

[jwl]

My guess would be that the sonic screwdriver can screw up high tech. weaponry but is less effective against a more simple mechanical device.

That or he simply didn't have it out and ready to go when the Secret Service caught him (I don't recall), and didn't want to trust his ability to activate it faster than a Secret Service agent could pull a trigger.

Also, sentinels are kind of shit too. No substantial ranged weapons to the best of my recollections. They have to be right on top of a ship to attack it.

Edit: Although that raises another interesting question- what is the range limit on a sonic screwdriver?

Well, aside from the Silurians, has the Doctor disabled other weapons with the sonic screwdriver? I don't remember him ever doing so against a Cyberman's weapons, or a Dalek's, a Sontaran, etc.

If he has, great, then in the words of Scotty, "The more they overthink the plumbing, the easier it is to stop up the drain."

If not, maybe Silurian weapons are just crap.

If I remember correctly, Sarah Jane disabled a (futuristic) weapon with her sonic lipstick in invasion of the bane.

[Simon_Jester]

The Doctor manipulating the Matrix... would be fun to see, yes. Potentially quite comical.

Well, aside from the Silurians, has the Doctor disabled other weapons with the sonic screwdriver? I don't remember him ever doing so against a Cyberman's weapons, or a Dalek's, a Sontaran, etc.

If he has, great, then in the words of Scotty, "The more they overthink the plumbing, the easier it is to stop up the drain."

If not, maybe Silurian weapons are just crap.

I think there's sort of... something like the uncanny valley effect in play.

A sonic screwdriver can't do much to interfere with the workings of, say, a stone hand-axe. It's a sharp rock on a stick; there's no electrical circuitry to interfere with, no delicate parts to freeze in place by remote mechanisms. Even given time to whip out the sonic and play with it, there's no guarantee the Doctor could do anything to stop a caveman with a stone axe.

At the other end of the scale, the Daleks have immense technological sophistication and have every reason to put a vast amount of effort into specifically countering Time Lord technology. It's not surprising that you can't easily use a sonic screwdriver to interfere with their machines; they have technology capable of matching what it can do and are highly familiar with its operating principles. Presumably they can shield against it.

In the middle, you have devices like the Sontaran weapons. Things that are sophisticated enough to be interfered with, but not sophisticated enough to be immune to tampering from the Time Lord version of a Swiss Army knife (i.e. a tool that manipulates force fields, resonates with mechanisms, interacts with electronic circuitry and can make it dance funny little jigs at will, and so on).

The only question is, does an automatic handgun fall into this "can be interfered with" category, or into the "stone axe" category...

[The Romulan Republic]

So, here's my take on how this might play out (bearing in mind that my knowledge of the Matrix is a bit incomplete beyond the first film):

I'm fairly confident in saying Eleven and possibly Twelve would stick around and ask questions, that the Nebuchadnezzar crew would detain them and any companions (barring successful use of the psychic paper, anyway, and I'm not sure how easy someone who saw through the Matrix would be to fool with that trick), but that Morpheus probably wouldn't kill them or chuck them overboard without questioning them first, and that Morpheus would likely go to the Oracle about it once he realized he was dealing with an actual alien (something unprecedented in his world). Meanwhile, the Doctor, being the Doctor, likely tries to chat with the crew (Eleven will probably be better at this than Twelve), and while some of them will probably keep their traps shut, Tank, Cypher, and Mouse, at least, might be talkative enough to let something slip. So the Doctor will likely piece together at least some of the situation, if not that the crew is looking for the One or what the One's role is.

This is where I'm lost, frankly. Because after that, how Morpheus deals with the Doctor will likely hinge heavily on what the Oracle says. If we presume that the Oracle has no knowledge of the Doctor, she'll likely fake it to keep up appearances, and may try to get Morpheus to eliminate him as an outside factor interfering in her schemes. Alternatively, she may not realize the level of interference he's capable of, and be largely indifferent to him. If she does have some knowledge of the Doctor, however (let's say that when the machines took over they got their hands on some UNIT/Torchwood files), then she'll likely want to a) avoid pissing him off, and b) incorporate him into her plans. So she'll likely ask to have him brought to her (or if that proves impossible, have a means set up to communicate with him indirectly).

If the former, the Doctor's in trouble. Morpheus and his crew won't hesitate to kill a threat on sight. In the other scenarios, the Doctor can probably work his way into Morpheus's good graces, though the readiness of his people to kill innocent humans while fighting in the Matrix might be a sore point. Eleven and Twelve though would maybe, grudgingly at least, accept it as necessary at times, due to the risk of people being taken over by Agents, and blame the machines. Ten would likely lose it at Morpheus and company, at least in his later episodes. He didn't take kindly to guns.

Of course, this will be going on alongside the hunt for the One, and with the Agents closing in on him, Morpheus will probably prioritize that. There were some close calls there, so the Doctor's presence might easily make things better or worse via the butterfly effect. The Doctor probably won't be able to talk his way onto that mission even if he wants to, though, unless the Oracle pushes Morpheus to trust him/work with him. But he might prefer, once he's filled in on the origins of the current situation (insofar as the resistance knows it), to confront the machine leadership directly in the real world and try to negotiate a solution. That's the kind of situation where he's in his element- the Doctor accomplishes more via technobable or diplomacy than he does in a direct fight, as a rule.

I think we've already covered the topic of how the Doctor might handle the Matrix, but its a bit difficult to be sure what the limits will be for him. But yes, like Simon_Jester said, it would probably be fun to watch. And I'd rather enjoy seeing the Doctor conversing with Agent Smith- I feel like Smith might make a good straight man for the Doctor to play off of (especially Eleven).

It would be interesting if the Doctor was onboard when Cypher pulled his betrayal, though. Cypher could probably get the drop on him, and most likely, the weapon Cypher used on the crew would trigger a regeneration.

God help Cypher if he murders Amy or Rory though.

If the Doctor can shut down the Matrix/sentinels or negotiate a ceasefire, then its just a matter of dealing with the clouds. I'm not sure what his chances are at either though. But I think he would try to help, most likely.

One thing I do know about the backstory is that the humans had a lot of blame for the war. Oh, and they scorched the sky. The Doctor will probably go off on one of his "stupid human" rants over both of those.

[NecronLord]

Do the machines have any forces outside of the Matrix besides sentinels (flying shit as far as serious combat is concerned) and the artillery you mentioned?

Yes, they do. The Animatrix historical footage shows they had a full combined arms force including infantry bots, planebots, tankbots, nuclear weapons, titan-scale harvester bots, and more.

That was obviously hundreds of years ago, but we've no evidence they've been decommissioned; they send only sentinels to the war but sentinels are more than enough and destroying Zion is basically a policing operation; you don't see the full panoply of the US war machine when they send riot police somewhere.

The Wachowskis have also said that the games form part of the official story and I believe some of them have yet more killbots.

I can't imagine the artillery being a big issue for the Doctor. Even if he did decide to venture within its range, artillery isn't generally intended to take out lone infiltrators, and in any case he'd likely approach aboard the TARDIS, which has some fairly impressive shielding.

They don't immediately call out the guard when Neo crashes a ship into the city either, so I imagine the Doctor could get out of the TARDIS and look around for some time before being detained.

A lone sentinel might or might not be able to take him. Against a sentinel swarm... he'd likely be as vulnerable as anyone else I imagine, unless the sonic screwdriver can be effective at much greater ranges than I recall or he's had time to prepare some sort of defence.

As to how he'd fair in the Matrix, the point about the Valeyard is interesting, and not something I was aware of (I've never seen those episodes). However, I must point out that the way the Matrix operates seems to be less about innate ability and more about state of mind. In other words, presuming he can function in the Matrix like a human can at all (differences in Time Lord brains, after all),

Glitz is human in the Time Lord Matrix. We also see humans in a Time Lord matrix in the recent episode where Missy worked with the cybermen, where Missy had been harvesting people's minds at death; that was said to be a Gallifreyan Matrix core. The Time Lords' conciousness is harvested on death and uploaded to their matrix. It may be that the zero one matrix is inferior and incapable of handling a Time Lord mind, but they are conceptually very similar.

The Matrix on Gallifrey is a big deal in their culture, and the Keeper of the Matrix is a member of the Supreme Council; the Doctor would not be surprised by concept, though he might well consider using it as a prison to be abhorrent; or he might think it was a great way for the machines to end the war ("What's life? Nature's way of keeping meat fresh").

It's also notable that he survived, though it was touch and go, bonding with the Matrix Crown (the Crown of Rassilon) without preparation; Time Lord presidents usually have to meditate and prepare themselves before bonding with it. The Matrix Crown allows them to draw on the collective knowledge of the deceased Time Lords in the Matrix.

The problem won't be if he can't handle it, but if the Zero One matrix has the bandwidth for a Time Lord mind.

the Doctor ought to be able to manipulate the Matrix in the same ways that Neo and company do if he believes that he can, if he accepts that its not real, just computer code.

Almost certainly he will. Certainly if he knows he's going into it.

In that, I think he might actually have leg up on them. Maybe not on Neo, who's a one off anomaly, but on ordinary human rebels who have been freed from the Matrix. After all, the Doctor is accustomed to dealing with the strange, with things being not as they seem, and has that Time Lord mind to work with. Shaping reality with his thoughts is likely to be a concept that comes much more readily to him than the average human.

Edit: Although punching, kicking, and shooting generally isn't his style. I'd be interested to see how the Doctor would bend reality in the Matrix, because I dare say he'd try for something a bit more creative.

Notably he's able to refuse to drown, and resist physical injury in the Gallifreyan matrix. Opponents might try to beat him only to actually fail, or to have him teleport out of the way.

[NecronLord]

This is where I'm lost, frankly. Because after that, how Morpheus deals with the Doctor will likely hinge heavily on what the Oracle says. If we presume that the Oracle has no knowledge of the Doctor, she'll likely fake it to keep up appearances, and may try to get Morpheus to eliminate him as an outside factor interfering in her schemes. Alternatively, she may not realize the level of interference he's capable of, and be largely indifferent to him. If she does have some knowledge of the Doctor, however (let's say that when the machines took over they got their hands on some UNIT/Torchwood files), then she'll likely want to a) avoid pissing him off, and b) incorporate him into her plans. So she'll likely ask to have him brought to her (or if that proves impossible, have a means set up to communicate with him indirectly).

I find it hard to imagine the Oracle asking for anyone to be murdered. She's not that casual about intelligent life.

If the Doctor can shut down the Matrix/sentinels or negotiate a ceasefire, then its just a matter of dealing with the clouds. I'm not sure what his chances are at either though. But I think he would try to help, most likely.

100% if he wants to.

He is if nothing else able to operate advanced terraforming equipment, and if nothing else he can always just give the machines books out of the TARDIS library on the topic.