For the S4 premiere the VOY crew, League and Conclave are wondering what they heck they're going to do now with the possibility of the Deep-Beta Quadrant becoming the battlefield for an all-out Borg-Fluidic War. The VOY crew in particular are alarmed because to them this is the beginning of the dark future they experienced when they were hurled 30 years into the future in “Tomorrow’s Voyager”.
Also, the VOY crew wonder what to do with the drone they picked up, since the Fluidic overload that killed the Sphere also terminated her connection to the Collective. Janeway decides that since she's not Borg anymore she gets to live, but under heavy security.
While trying to help Harry, the Vidiians try several new medical treatments they used in the last Fluidic Invasion to try and combat the Fluidic DNA infestation. They get the idea that a nanite attack may work, so they extract some from Seven (who's still semi-conscious) and experiment until they got it since Borg technology has the only nanites advanced enough.
They then find out from the League that there's a bigger build-up of dimensional rift energies (the energy given off whenever the Fluidics enter or exist those dimensional rifts they can make) and the Fluidics are using them to enter a variation of their home Fluidic Space (which is kind of like B5 Hyperspace in this version) to travel without being detected and then attack the Borg in regular space when they re-emerge. The readings aren’t exactly the same as from the Fluidic Wars, meaning they can’t make a rift back to the original Fluidic Space they emerged from for some reason.
They track the battles down, coming across lots of smaller Borg ships that have been damaged or destroyed and lots of dead Fluidic bioships as well (they're equally matched) until they find out the Borg have assimilated an entire planet as the scout force's Base of Operations.
They're trying to build a Transwarp gateway on this side so they can summon unlimited Borg reinforcements from the Delta Quadrant (since the Transwarp Conduit the Scout force used to arrive was more or less a one-way shot).
Janeway then decides to wait until the Fluidics have overwhelmed the Borg Scout force (which is only one Cube and maybe a few smaller probe ships and that one Sphere that was destroyed earlier) and use their planetkiller attack to destroy the Borg planet.
Seven tries to stop them when she wakes up, breaking out of sickbay and into engineering, but the crew manage to stop her (maybe Kes with her TK holds her in place without having to touch her). With the last of the Borg in this quadrant gone she goes despondent.
VOY tests out the nanites as a weapon on the Fluidic ships which destroys them. While the Fluidics pull back to analyze their destroyed ships' to find out what the heck happened Voyager and the combined Conclave/League fleet retreat.
It's postulated that the Fluidics may find a way to neutralize the nanites, but at least now the Conclave have a weapon that once again works on the Fluidics. The League wants it but the Conclave then puts them in their place saying that they need it for further research, and if the League tries anything they'll destroy the nanites and all their data on them. The League isn’t willing to call their bluff.
The Doctor then gives them the sad news that while they were able to create the nanite weapon from their treatment of Harry, it was too late to save him and he had died from the Fluidic DNA infection.
Secretly the Conclave gives the nanotech data to VOY for safekeeping, and with that and their new crewmate (Seven) as well as the Concave delegation waiting to make contact with the Federation, VOY activates the Slipstream Drive and sets a course for their last friendly location, DS9.
However, since this is around 2375/2376, they have a surprise waiting for them back in the Alpha Quadrant...
Kes by this point is now a full adult (she was a 10 year in S1, a young teenager in S2, about 17 in S3 and by S4 she's early to mid twenties). She also has more control over her Telepathy and Telekinesis, and as a side-effect of being exposed to chroniton radiation in "Year of Hell" she now has occasion telepathic flashes of the future (she sees through her future self’s eyes or even is projected into her future self at times).
This version of Seven wouldn't be the "I want to go back to the Collective" version but more like a combo of Hugh and maybe Kai from LEXX since her past memories are totally gone and she wasn't openly conscious of what was happening to her all these years. She wouldn't even remember her human name (and how a human who wasn't from Wolf 359 got to the Borg years before Wolf would be a mystery). Her skin color and hair start to grow back but other implants stay in just so the Feds don't accidentally activate that Borg self-destruct.