VOY goes back to the Alpha Quadrant using the Slipstream Drive and plot co-ordinates that will land them near DS9. When they get there their scanners detect over ten times the normal amount of vessels than should be there, including Romulan Warbirds.
Wondering what the hell is going on, and receiving some Fed messages about wartime status they fear that it's a Romulan Invasion and in the state they're in (powering up the Slipstream Drive took up almost all power except for what they could spare for life-support and basic stuff) a light Cardassian ship would take them out.
But then they see the Romulans arriving to pick them up along with Fed and Klingon ships, they're more confused than before when the Fed Admiral (Ross?) mentions "Good thing we picked you up before the Jem'Hadar did."
Next would be a homecoming episode where the VOY crew are taken to Earth for debriefing. They learn about the Dominion, the Cardassian alliance, and the destruction of the Maquis. Chakotay and the surviving Maquis take this hard and to make matters worse they realize now they're likely to just end up in prison for their actions prior to being on VOY.
But Starfleet tells them that Janeway spoke up on their behalf, and more importantly Denara Pel and the Conclave delegation also spoke up for them and the Feds are willing to make concessions in exchange for peaceful relations with a new potential ally.
Tom would then go (with Kes) to tell Harry's family about what happened to him, while B'Ellana's family would learn of how they now had three daughters and two are dead. The Doctor would undergo examination for his sentience and Seven of Nine would be a big point of interest.
Going over everything VOY encountered in the Beta Quadrant, especially the Fluidics, Starfleet wonders what to do especially with the Dominion situation happening now. They also are studying the Slipstream drive.
Due to their services Locarno/Paris is granted an official commission and the Maquis are granted Amnesty. Chakotay decides to re-enlist to fight the Dominion, Denara and co are put on maximum security to keep them safe from potential Dominion assassination or capture. B'Ellana decides to just resign as she's been through enough and is grateful to be home, the whole experience having helped her reconcile with her issues over her hybrid nature. Tuvok sees his family on Vulcan.
I think I'd do something radically different and have Seven revealed to be Annika Ransom, daughter of the missing Captain Ransom, who was lost years ago when Ransom's wife took Annika with her on a science mission and never returned (like the Hanson's in Seven's official backstory). Seven wouldn't really feel that bad since she doesn't remember her father at all and she's mad at her mom for endangering her.
We jump one year ahead with a text explanation of how Janeway, Tom, Tuvok and Chakotay fought in the Dominion War and are now recalled to Starfleet HQ for a new mission.
They're surprised to see each other again (they all fought separately). Tom is a Lt. Cmdr, Chakotay is a full Commander and Janeway received a promotion to Captain and is in command red now, having had her own ship in the war.
They learn that Starfleet has decided to make Voyager into a sort of memorial ship/museum ship since it was near the end of its operational lifespan anyways and was really jury-rigged from the Vidiian, Talaxian and Krenim tech they grafted onto it to make repairs. They took out the Slipstream Drive to study and have discovered that the resources that help stabilize and power it (which is different from Dilithium) don't exist in the Alpha Quadrant. They're able to synthesize it but not in large enough amounts to mass-produce the Slipstream Drive.
They have built some smaller ships for testing their own Slipstream drives and have constructed large mining/transport vessels while speaking with the Conclave Delegation. They've agreed to open relations with the Alpha Quadrant and will return to the Deep-Beta Quadrant now so to help in opening trade negotiations for the resources needed in the Slipstream Drive. Starfleet has prepared a new vessel to escort them home and the Conclave Delegation have requested that the crew of VOY be in command.
VOY has enough of the synthesized Slipstream material for 2 Slipstream usages: 1 to go back to the Deep-Beta Quadrant and 1 to go back home to deliver a status report of whether they were successful or not in gaining access to the needed resources.
The crew agree and Starfleet christens their new vessel, a new class known as the "Intrepid-class", "Voyager" in honour of its predecessor.
And so Captain Janeway, 1st Officer Chakotay, Helmsman Lt-Cmdr Paris, Tactical Officer Lt-Cmdr Tuvok, Science Officer Seven, the Doctor (uploaded from the Old VOY to the New VOY) and Kes take off to go back to the Deep-Beta Quadrant with their new mission.