Okay, so a possible plot-outline, combining my idea, elements of Star Trek Online, as well as elements of bilateraltrope's, and maybe a bit of SFDebris' take on Voyager and Janeway, at least the less obviously parody parts (mostly the idea of a guilt-ridden Janeway who snapped under her struggles in the Delta Quadrant).
Star Trek: Voyager: The Movie.
Scene One: Big action opening as Starfleet Command awaits a Borg attack. Transwarp conduit opens, Borg Cube comes flying out... and then Voyager emerges from its debris. The end of the show, but with a bigger effects budget and from a different point of view.
Scene Two: Everyone is discussing Voyager's return. We cut to a courtroom, where Janeway is being debriefed over various incidents during her ship's journey. The judges agree that she acted questionably at times, but that her heroic acts in bringing her crew home and crippling or destroying the Borg are enough to absolve her, especially since the public views her and her crew as heroes. Janeway is pardoned, along with the Marquis crew members.
Scene Three: Janeway says goodbye to Chakotay and the other crew. She's getting a promotion to Admiral and an office at Starfleet Command, Voyager is being picked apart for useful information, then possibly turned into a museum piece. Chakotay is pardoned and will be made First Officer on another ship. Most of the Marquis are going with him. Tom Paris is pardoned, and is getting a promotion. Harry Kim is finally getting promoted too. Seven is being fast-tracked to join Starfleet if she wishes. Promotions all around. A bit of sadness over the people who moved on while they were away. Bittersweet ending.
Scene Four: The destruction of Romulus, some years later. We watch as Sela and the other Romulan leaders evacuate. Sela makes sure the other leaders don't make it out, and assumes command of the survivors.
Scene Five: A Voyager reunion party, catching up on the various crew a few years later. Party is interrupted when Janeway gets a call about the destruction of Romulus and Sela's taking power. We can namedrop the Iconians here as foreshadowing- say Chakotay (who has an interest in archaeology canonically as I recall) has been studying their artifacts. Maybe rumours about a hidden Iconian remnant, which is believed to be a myth a la Atlantis.
Scene Six: Briefing with various Starfleet bigwigs. They report some highly-classified information: that the supernova which destroyed Romulus appeared to be triggered artificially, before it naturally would have happened, maximizing the destruction. Starfleet covert operatives believe the weapon matches a technology that Janeway encountered in the Delta Quadrant. Starfleet questions her, and decides to send a covert team into Romulan space to investigate what happened, and see if Sela is working with someone in the Delta Quadrant.
Janeway recommends Chakotay (now a Captain, with Tom Paris as his XO), to command the team. Most of the old Voyager crew will be coming along: Be'lanna as Chief Engineer, the Doctor as... the Doctor, Harry Kim (now a Lt. Commander) as Science Officer, Icheb as Ops officer or something, Tuvok commanding a squad of Starfleet commandoes, and a new Helmsman character. Voyager, which is no longer official on active duty but remains space-worthy and is outfitted with various rare technologies that Janeway acquired in the Delta Quadrant, will be brought out of retirement for the mission.
Scene Seven: Voyager is being prepared for launch. Chakotay is on the bridge. Janeway calls in to wish them good luck- she'll be running things from Starfleet command. The fleet is making a show of force along the old Neutral Zone to deter vengeful Romulans who blame the Federation, while also extended the olive branch of humanitarian aid. Under cover of this operation, Chakotay's crew will slip in undetected (their ship has been equipped with an experimental cloak, since with the collapse of the Romulans as a power, no one gives a damn about the anti-cloaking treaty any more). Seven of Nine arrives at the last moment as a civilian consultant. Since Chakotay and her broke up a while ago (first relationships, particularly developed on the spur of the moment, tend not to last), this is awkward for both of them, though both try to focus on doing their duty.
Scene Eight: Voyager en route to the Neutral Zone. Chakotay has an awkward conversation with Seven in the mess hall. They agree that its best they not try to start things over, and just focus on getting the job done.
Scene Nine: They arrive at the Neutral Zone, and are greeted by the fleet. Beaming down, they find themselves in a colony that's been turned into a forward base for shipping aid to the Romulans, and processing Romulan refugees. They cross paths with some of the DS9 crew here (inter-film crossover), who give them useful intelligence on how to break into Sela's HQ and locate the data on the weapon that destroyed Romulus, and shield frequencies to penetrate the defences. They also hear reports of Spock's disappearance (a nod to the '09 film), and rumours of a new Romulan splinter group calling themselves the Romulan Republic.
Scene Ten: The meeting is interrupted by an attack by a fleet of Romulan radicals. During the battle, Voyager slips into Romulan space undetected.
Scene Eleven: Final briefing before the operation, everyone is given their assignments. Tom, Harry, and Tuvok will beam down, along with some commandoes.
Scene Twelve: Voyager slips past some Romulan patrols, and the strike team beams down.
Scene Thirteen: Inside the base, they encounter prisoners- Romulan dissidents and Reman slaves, being held in inhumane conditions. Harry and Tom want to try to break them out, but Tuvok reminds them that this is not their mission. They break into the data storage facility as planned.
Scene Fourteen: They manage to access data proving that Sela is in contact with a Delta Quadrant power. However, they trip an alarm and guards begin to arrive. They fight their way to the extraction point and... can't beam out. The shield frequency has been changed. They surrender.
Scene Fifteen: Sela meets with her advisors, who warn her about the growing threat from Remin and Romulan rebels- colonies that have broken off from the failed Romulan government and are appealing to the Federation for help. Sela, believing Tom is working with them, decides to interrogate him.
Scene Sixteen: Sela interrogates Tom, who refuses to break. She tells him that she will begin executing one of his team every hour until he reveals everything to her.
Scene Seventeen: In their prisoner barracks, the other members of the team begin to talk to the Romulan and Reman captives. They promise to give them asylum in the Federation if they cooperate to help overpower the guards and escape. The other captives are initially reluctant to trust Starfleet, and the first of the team is taken to be executed.
Scene Eighteen: Cut back to Starfleet Command. Janeway has gotten a report from Chakotay that Tom's team is overdue, and the shield frequencies have been changed. Chakotay requests permission to attempt a rescue. Janeway denies him permission, though she is clearly guilt-ridden about abandoning members of her crew. Chakotay is angry over abandoning the crew, but most of all over abandoning Seven. Janeway accuses him of being blinded by his feelings. He reminds Janeway of how she risked a raid into Borg space to save Seven before. She counters that she is an admiral now, back in Federation space, no longer on her own but accountable to Starfleet oversight. It clearly brings back a lot of bad memories, however, of all the people Janeway lost in the Delta Quadrant. She decides to talk to the other Admirals to see if anything can be done.
Scene Nineteen: The guards come to execute another prisoner. Nearly half the team is gone. Tuvok mind-melds with one of the Romulans to convince them of the Voyager team's trustworthiness. When the next guard comes, Seven uses her Borg nano-probes to overcome the security systems, and the rebels swarm and overpower the guards, though many are killed.
Scene Twenty: Sela is busy gloating to Tom. We get some insight into her character and motivations here- her career has stalled due to repeated failures, and she sees this coup as the only way to advance herself, and to expunge the shame of her part-human heritage by defeating the Federation. Tom, as both a Federation officer and a father and husband of part-humans, naturally argues this point. Sela is close to losing it completely, but is interrupted by a red alert, followed by one of her guards rushing in to warn her that the base is being overrun. Sela draws a disruptor to shoot Tom, but is interrupted by the guard being shot in the back as Tuvok and the others arrive. They free Tom, but Sela beams out, escaping aboard her command ship.
Scene Twenty One: Sela orders her ship to fire on the base, killing everyone inside and destroying the evidence of her crimes. However, she is interrupted by Voyager- Chakotay could not disobey orders directly, but stalled, hoping for a chance to intervene. Once the battle broke out below, that gave him the excuse to act. Its still a lop-sided fight, especially once another squad of Romulan ships decloaks- until they open fire on Sela. The ships hail Voyager, identifying themselves as vessels of the Romulan Republic, which Starfleet has now recognized as a legitimate government of the Romulans. Janeway is onboard as well, having contacted the Federation's new allies for assistance in rescuing her crew. The survivors from the base are beamed up, and Chakotay's relief at Seven's safety is obvious, much to her discomfort.
Sela escapes via transwarp.
Scene Twenty Two: Meeting between the Republic and Starfleet on the new Republic flagship. They have examined the data from Sela's HQ, and have concluded that she collaborated with a power in the Delta Quadrant which destroyed Romulus, though it is unclear if Sela knew that that was the plan or was simply an unwitting pawn. It is decided to use an experimental new transwarp drive, based on Borg tech. Voyager captured in the Delta Quadrant, so that Voyager can return there, and establish a permanent Starfleet presence. The Romulan Republic requests to send a detachment with Voyager, since capturing Sela is an internal Romulan matter.
Scene Twenty Three: Voyager activates the transwarp drive.
Scene Twenty Four: Janeway and Chakotay make up, acknowledging that both had a point in their prior argument. They also discuss their misgivings over returning to the Delta Quadrant, reflecting on the painful (and positive) memories the prospect brings, and wondering what long-term effects their presence had. They are interrupted by Seven, and Janeway politely excuses herself.
Chakotay and Seven talk, and admit that they still have feelings for one another. However, they are reluctant to try again- Seven in particular is still hurt by the failure of her first real romance, and Chakotay does not wish to hurt her again.
Scene Twenty Five: The crew arrives over the Talaxian colony where they left Neelix, which was selected as a good place to figure out what's gone on in the Delta Quadrant since they were last there, to find it under attack by aliens (maybe the Hirogen?). Voyager chases them off, then hail the colony and are greeted by a disheveled, and very surprised, Neelix.
Scene Twenty Six: The crew beams down to the colony to offer aid. We see here our first glimpse of a more mature and authoritative Neelix, shaped by having to spend years defending and his colony.
Scene Twenty Seven: A conference occurs with Neelix and other leaders of the colony. He relates that, following the destruction of the Borg, a chaotic series of conflicts occurred as various powers attempted to fill the power vacuum, though some force seems to be playing the factions off each other, ensuring none becomes all-powerful. Neelix did what he could to help the refugees, but his small colony was overwhelmed, and could usually only survive by paying off the invader of the week. Janeway is disturbed by the consequences of her actions, though Neelix tries to assure her that he doesn't blame her.
Scene Twenty Eight: Long-range sensors have traced Sela's transwarp signature to a seemingly-uninhabited system. The pursuit is on. They arrive to find Sela's warbird in orbit, damaged. Chakotay notes that the ruins on the surface match the Iconians. Janeway wants to hail it and offer it a chance to surrender, in accordance with Federation regs. Chakotay and the Romulans note that Sela has already proven hostile and still outguns them. The Romulans point out that capturing Sela is a Romulan matter where the Federation is assisting them, and that Romulan regs. call for dropping cloak and opening fire at once. Janeway reluctantly complies. Sela's ship is crippled.
Scene Twenty Nine: The crew board, to find the vessel mostly deserted. Their are indications, however, that Sela has beamed down to the surface. They pursue.
Scene Thirty: Cut to Sela on the planets' surface. It is covered in strange, unfamiliar ruins. Sela is following a signal from her unknown ally, to a temple/control room at the centre of the planet. Upon reaching it, they activate a holoprojector, with a message: this planet was the last stronghold of the Iconians, now overseen by an AI, with instructions to find a worthy ally among the lesser races of the galaxy who could reactivate the Iconian gates, bringing the ancient Iconians back. Sela, warned by her subordinates that the pursuit is just behind them, decides that it is her only chance. She activates the gate, and goes through.
Scene Thirty One: The Voyager team enters the facility. Seven and Harry between them are able to access the Iconian database, and open the gate as well. They also activate a holorecording, which reveals the true plan of the Iconians- we do not see the plan, just the crew's horrified reaction.
Scene Thirty Two: Cut briefly back to Voyager, as a Hirogen fleet arrives, seeking vengeance. Voyager fights back, but is overwhelmed.
Scene Thirty Three: Sela stands in the place between worlds, an extra-dimensional nexus linking all of the Iconian gates. She is about to activate the gates when the Voyager team arrives. They try to talk her down, but Sela begins ranting about how this will make up for all of her past failures. Janeway tries to reach her, telling her that the important thing is to learn from your mistakes, to try to fix them, not to let them define you. Sela isn't listening, though. So they play their trump card: the recording of the Iconian plan they uncovered. To divide the galaxy though endless warfare among the "inferior races", then open the gateways so that the Iconians could return from their hibernation. We see glimpses of various events that the Iconians were tied to- the Dominion War, Species 8472, the destruction of Romulus...
Sela is horrified, realizing she has been played. She decides to surrender. But then, suddenly, one of the Voyager team runs forward and activates the gates. The Iconians have been playing a long game, and have agents in more than one power.
Scene Thirty Three: The Iconians' automated defences begin to activate. The Voyager and Romulan forces attempt to fleet, planning to beam up and order a quantum torpedo strike on the Iconian base, only to find that Voyager is not responding to hails. Cut back to Voyager, where Chakotay's command is burning around him. He gives the order to beam down to the surface, then sets Voyager to ram the lead Hirogen ship.
Scene Thirty Four: On the ground, the crews realize that they are stranded. Seven, though broken-hearted over Chakotay's death, believes that she can activate one of the Iconian gates, allowing them to return to the Alpha Quadrant. The others will attempt to hold off the Iconian defences until she can. But someone will have to stay behind to operate the gate, and detonate explosives to ensure that it is destroyed. Sela, in an effort to redeem herself (or escape custody) volunteers. The survivors make it through, and Sela detonates the explosives, though it is left ambiguous weather she died.
Scene Thirty Five: Memorial for Chakotay at Starfleet HQ. Janeway speaks. After the memorial, she informs her senior officers that now that the Iconian gateways have opened, the galaxy will become more united. It will have to, because their are still Iconian forces out their, seeking to divide them. To that end, she is being made Federation Commander in the Delta Quadrant, and requests that they rejoin her. They accept, Seven expressing hope that Chakotay somehow escaped Voyager's destruction.
End Credits.
There's a lot I'm not sure about due to fear of cliche, especially the Seven/Chakotay romance stuff, Chakotay's death, and Sela's death, but presuming each scene averages five minutes of screen-time, we're talking a three-hour film (could probably be tweaked to be significantly shorter) that should be reasonably coherent.
DS9 Outline to come!
