Kes would take over as a second Doctor on the ship, as Ocampa maturation is also faster mentally and she studied as the Ship Nurse long enough to take in Federation Medical knowledge. By this point she’d be physically in her mid-twenties and now played be Jennifer Lien.
The crew would have to deal with the fact that the child they used to all see as a younger sister or even a daughter (in Janeway's case, for example) is now an adult just as mature and intelligent as them or even more mature and intelligent as them in some cases.
Tom would have to deal with his attraction to her because to him she was only a kid when they first met.
After helping to go through old Conclave technology and databanks that the Vaadwaur and Vidiians held onto (since Federation technology is the result of several races putting their sciences together it’s the similar basis for the Old Conclave’s multi-species sciences) VOY uploads some old Conclave Starmaps onto the Astrometrics computers. When combined with the Federation Starcharts they figure out that they're in the Beta Quadrant, but 30,000 LY from the edge of the known BQ so the area they're in is now designated the "Deep-Beta Quadrant".
The Ocampa are allowed into the Neo-Conclave at Kes' request so they can have some telepaths/telekinetics and Kes' people can be properly aided in surviving without the Caretaker. This causes tensions with the Devore Empire due to their anti-telepath stance.
Year of Hell
The Neo-Conclave is then contacted by the Krenim Imperial Family who request their aid in stopping their civil war.
They decide to intervene when the Imperial Family tell them about who is leading the military revolt and what kind of power he wields:
The Krenim people are a society who consider existence to be one big equation that they seek to manipulate and add new variables to in order to create their ideal future. They have this machine they found on ancient ruins of an extinct elder race that basically is a very accurate simulation predictor: It takes into account all available data on everything and shows you the most probable outcome. They used it to make the Krenim a powerful empire by identifying whatever variables can threaten them, then destroy/alter/remove those variables (alien races that may become future rivals, Krenim who can become dangerous revolutionaries, etc).
One of their best minds, a military scientist named Annorax studied the device and used the temporal knowledge to eventually develop temporal technologies and stuff that have made the Krenim a major power that most don't cross other than the unlucky guys who get conquered/defeated because they're "unstable variables in the equation".
Annorax's greatest achievement is the timeship weapon, which can only be used sparingly (the core uses vast amounts of power and takes a long time to recharge for a full incursion) and he built it as an anti-Fluidic weapon to defend themselves with.
The Imperial Family tell the Conclave that Annorax eventually just became full of himself and started the military coup to take over the Imperium, and he armed the forces loyal to him with temporal weapons he designed based on information he gained from the artifact, like the Chroniton warheads and stuff. So even though they are outnumbered from the forces loyal to the Imperial Family, they have superior weapons and are winning in battle.
VOY and the Conclave get involved due to the extreme danger the Timeship poses and what kind of damage it could do to the time-space continuum, but since the Talaxians are still rebuilding and the Vidiians and Kazon are spread out thinly protecting Talaxian space and the other new worlds of the Neo-Conclave, VOY is barely able to match the Annorax Krenim’s numbers with what available Vidiian, Kazon, Talaxian and Vaadwaur ships there are, but the tables are turned when they combine with what remains of the Krenim Loyalist faction. The League occasional help out.
Things go okay for a while until Annorax "deletes" other races, changing the timeline so now VOY and their side are getting trashed in continuous battle until they manage to find a way to create temporal shields like they did in-canon, and give this information to the Krenim loyalists. They then encounter Annorax himself with his Timeship and learns the whole truth: Annorax originally built the Timeship as a last resort anti-Fluidic weapon, but under heavy pressure from the Imperial Family politicians and the military he was forced into using it on the Rilnar, whom the Krenim were in a losing war with. He succeeded in erasing them and turning the Krenim Empire into an even stronger power but it also erased his family and their home colony world. Millions of Krenim also ended up dying from plagues they were immune to in the original timeline because of antibodies they got from the Rilnar (who no longer exist), like in the original TV story. When he returned to the Krenim Imperials and told them of what happened (they didn't remember, as they were also affected by the time change) he begged them to let him keep using the Timeship to try and restore his family and those lost, but the Imperials were horrified at the true power of the Timeship and ordered Annorax to cease.
In his grief he launched his coup to take over so that he could guide the Krenim destiny and restore what was taken from him and began erasing other races as well. So the Imperial family’s abuse of the Anti-Fluidic tech and the twisting of Annorax's good intentions is what really caused this mess to begin with.
During one battle near the end of the Krenim War arc, the first experimental temporal shields that VOY creates to counter Annorax's weapons reacts with a temporal warhead/photon torpedo exchange and opens a temporal rift that sucks VOY 30 years into the future.
Once there they find that in this future the Borg assimilated the Fluidics but instead of just absorbing them the Fluidics’ own collective mind merged with the Borg one, creating a hybrid race one that has inherited the Fluidics' xenocidal desires and the power/infrastructure of the Borg Collective, meaning the Borg/Fluidics have been using all their power to destroy everything they encounter instead of just assimilating what they think is worth it. The Neo-Conclave and League have been all but destroyed and the remnants of the Alpha Quadrant powers are desperately fighting off endless Borg/Fluidic attacks (they're busying attacking the whole galaxy so they can't focus entirely on the small area of the Alpha/Beta Quadrants Trek takes place in).
So when they get back through the time warp and back to the Krenim war they have more of a reason to help out in the Fluidics situation.
In the end they succeed in destroying the Timeship, but VOY and the Imperial Flagship keep their time-shields up so they are unaffected by the change back to the original timeline. The Imperial Family remember everything and so do VOY (so whatever damage they took is still there, and whatever permanent injuries crewmembers took is still there, etc), Annorax is reunited with his wife and stuff only in the revised timeline he never built the Timeship, so the Krenim Imperium isn't the Megapower it was, but is still a great power due to the Temporal Weapons Annorax did build (Chroniton Warheads and stuff, still exist) and the deleted races are back.
The Krenim join the Conclave out of gratitude, but agree not to develop anything like the Timeship again, burying such dangerous knowledge.
And the ancient artifact the Krenim civilization has been guided by is revealed in the end as the same "species" as the Guardian of Forever.