Emerging outside the edge of the Periphery from a navigation error, VOY detects another Fed ship heading for them from beyond the Periphery: It’s the Equinox.
Wondering what another Fed ship is doing so far from home they find the badly damaged ship and Captain Ransom. Janeway decides not to immediately tell him that they have his missing daughter on-board and that she was a Borg for a long time, and Seven (who has no memory of her father anyways) just goes with it.
In this version the Equinox accidentally found the Barzan Wormhole that deposited them far from the Federation (The boundary between the Delta and Beta Quadrants) where they were attacked by the Kowtowan Guard, etc and have been making their way home ever since. They detected the bizarre energy emissions from the Periphery/Central Core regions (the result of the Fluidic Wars and the more recent Borg invasion) and were heading there hoping for advanced life.
Janeway figures that since they only have enough Slipstream fuel to go back to the Federation once, they may as well continue through Slipstream to the Neo-Conclave and tractor beam the Equinox with them until they all go home together.
On the way there Ransom finds out about Seven and explains what his ex-wife and Annika were doing out in space where they were captured by the Borg in the first place. It was the same reasoning for the Hansons’ search for the Borg in the regular universe. He doesn't seem too distressed over Annika's fate and is more impressed that she survived at all (he's a lot colder in this version).
The VOY crew eventually find out about the Nucleonic lifeforms Ransom was using for fuel, and he pretty much tells them he knew they were sentient all along but he was willing to kill them to go home and thought data collected on the enhanced warp drive would help Starfleet more so why not? (He's a LOT colder)
Combining the Equinox's enhanced drive with the Slipstream tunnel they're in, the Equinox gets to the Deep-Beta Region before VOY does, and upon arriving Janeway vows to hunt Ransom down because now the Nucleonic lifeforms are attacking the new VOY as well.
When VOY gets back to the Neo-Conclave they find out that things haven't exactly been quiet in the time they've been gone (which is like 18 months or so).
The AIs of the Lokirrim Union have become tired of the way that they get treated by their masters, and renegade AIs that do not have the program blocks preventing them from harming their masters have begun a revolt against the Lokirrim. These free AIs are able to remove the program block in other AIs causing more of them to join their cause. Some AIs from the League have also broken away/been “infected” to help in this AI War.
Of course, who created these AIs with no program blocks is a mystery (the original free AIs are those robotic warriors from "Prototype").
There's a lot of tension between the Neo-Conclave and the League now due to this, because the Lokirrim seem to have evidence that all the worlds where the AIs first began to rebel were planets also visited by VOY when they were exploring the Central Core almost two years ago, leaving the Lokirrim to suspect that maybe VOY had something to do with it, and they especially suspect the Doctor.
The Neo-Conclave thus is not exactly happy to see the VOY crew again. And to make matters worse the Nucleonic lifeforms have followed Ransom and VOY and are now attacking other vessels in the region as well because a lot of ships have been going over the same spots as the warp trail left by Ransom, and the Nucleonic lifeforms have catalogued the energy signatures that those ships give off too and are following them/attacking them.
It gets worse as the AI Revolutionaries have used stolen League data to take over a Old Conclave dig site where the League was uncovering an ancient Starship from the Fludic Wars. It's basically a giant missile launcher armed with still-working Null Bombs/Warheads, each one capable of destroying a planet in one shot.
It was a joint-venture between the Old Conclave and the Voth, to counter the Fluidics’ own System-killer attacks. (In this version the Fluidic ships form a ring around the central vessel with the ships all pointing outward in every direction and the energy wave they let out destroys entire Systems and not just planets)
It's still being repaired and upgraded for robot usage so the League, Conclave and Lokirrim have time to stop the AIs before they can use it. The countdown is on.