I'd have Voyager encounter a seemingly abandoned, Borg transwarp network and face the dilemma of using it to return home and leaving it for the Borg to possibly return (and use it to conquer other species) or destroying it and taking their chances again. Janeway would be extremely reluctant this time, to make a decision either way and as she sends an away team to investigate the transwarp network, a Borg ship appears.
Voyager quickly beams the away team back and prepares for a fight with the Borg ship, but before a fight can break out they are hailed. The Borg Queen reveals that they detected Voyager entering the sector a few days ago and that they evacuated the transwarp hub with the intention of seeing what Janeway would do. The Queen would reveal that she is interested in Janeway and explains that she will allow the Voyager crew to return home, as long as Janeway stays (the alternative being assimilation).
Janeway agrees to the Queen's terms, but formulates a plan with the senior staff to destroy the Transwarp Hub as they are being escorted through it. The Doctor injects Janeway with the Neurolytic Pathogen and she beams aboard the Queen's ship. The Queen doesn't immediately assimilate her and reveals that she knew about the plan the whole time because they had placed a proximity transceiver device in Janeway the last time she was assimilated. The Doctor was unable to detect it during the removal of the implants and when the Queen arrived she activated it because she suspected a betrayal.
With that, the Queen orders the Sphere to intercept Voyager and assimilate them, but before the Sphere catches up, Seven of Nine appears behind the Queen and injects her with her assimilation tubules. Janeway is shocked at Seven's appearance and questions what she is doing there. Seven reveals that she detected the Borg proximity activation as a result of her latent connection to the hive mind, she formulated a plan with The Doctor using some form of code (or whatever). The Queen starts to break apart, as the realisation of the situation becomes clear - The Borg has been infected with the pathogen but Seven of Nine has Borg implants appearing on her. Somehow, the injection of the pathogen caused a feedback in Seven that has caused her to start changing back into a drone.
The Queen finds a way to tap into Seven and orders her to kill Janeway. After a fight where Seven has the upper hand, Janeway tries to appeal to the tiny part of individuality that Seven has left, she gets through and Seven shuts the Queen down and uses the link to the hive mind to destroy the sphere so Voyager can escape. She uses the link again and finds a way to activate the self destruct of the transwarp hub as she and Janeway run to the Delta Flyer. As they enter the gateway, the hub blows up and the Delta Flyer doesn't re-emerge with Voyager, leaving the fates of Seven and Janeway unknown.
Some time has passed following the celebration of the Voyager crew's return and a memorial service for Janeway and Seven. The crew of Voyager are at DS9, marking the anniversary of the ships launch on its first mission. As they reminisce about the time spent in the Delta Quadrant, a ship is detected emerging from the wormhole. It's the Delta Flyer and Janeway and Seven are both onboard. They reveal that the network collapsed and they fell out of transwarp in the Gamma Quadrant. They travelled for 6 months until they found the Bajoran Wormhole.
The episode concludes with Janeway being promoted to Admiral and the Doctor realising that Seven of Nine's link as the controller of the collective has restored her humanity, he can now remove the remaining implants and she can have full access to her emotions.
The End (or something like that)
- No Future Janeway.
- No overpowered future technology.
- The possibility that two of the shows main characters have died in the process of getting Voyager home.
- A nice, welcome and appropriate ending where Janeway gets home on the anniversary of her first mission.
- The same ambiguous end to the Borg collective.
And just for shits and giggles you could show everyone getting promotions, except Harry Kim who falls for it until Janeway personally presents him with his promotion and imparts some really emotional stuff.