I'm kinda of stuck at this point in where to go next. Because I've got it plotted out in one way, while the guys I've been working with on this think I should go another way.
My original idea was for the VOY crew to end up helping the Vidiians in the Talax liberation by locating other Talaxian cells throughout the Periphery, and also help in the "Conclave" plot by finding other species in the Periphery who may be willing to join and fit the "criteria" for joining (IE, a world/species the Vidiians may think need protecting from future Fluidic attacks, worlds that offer something to the new organization and aren't just a bunch of freeloaders) but not just letting in anyone and everyone becuase then it'll just be a mish-mash. But at the same time they can't be as picky or idealistic as the Feds are becuase the area of space (I've named it the Deep-Beta Quadrant) is a lot less peaceful and is more hard-edged than the Alpha Quadrant (this is before the Dominion War). They make a name for themselves by defeating the remaining Kazon pirates and maybe getting the non-Pirate Kazon Sects to join the Conclave as they aren't violent nuts like the now-deceased Cullah. The League isn't really concerned with them and don't see them as a threat so they just leave them to their own devices. The Ocampa are allowed in 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.
Then after that, the Neo-Conclave succeeds in freeing Talax and forcing the Haakonians to withdraw from Talaxian territories, end of S3. The Neo-Conclave is then contacted by the Krenim Imperial Family in S4 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 are a society who consider existence to be one big equation that they're always changing to better suit their ultimate 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 use it to make the Krenim a powerful empire by identifying whatever variables can threaten them, then destroy those variables (alien races that may become future rivals, Krenim who can become dangerous revolutionaries, etc).
One of their best scientists, a military officer 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 acheivement 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 become 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 Concalve 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 are spread out thinly protecting Talaxian space and the other new worlds of the Neo-Conclave, VOY is almost on its own aside from the forces of the Imperial Family and what available Vidiian ships there are. The League might eventually get involved too.
This is the S4 "Year of Hell" where VOY is involved in fighting the Krenim coup guys with the Krenim Loyalists and the Vidiians. Things go okay for a while until Annorax "deletes" other races, chaning the timeline so now VOY and their side are getting trashed in continous 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, turning the tide. They then encounter Annorax himself and his Timeship weapon capable of erasing whole things from time when fired at full power. VOY then learns the whole truth: Annorax originally did build the Timeship as and anti-Fluidic weapon, but under heavy pressure from the Imperial Family and polticians 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 a major power but it also erased his family and killed millions as in the original version. 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 and their abuse of the Anti-Fluidic tech and the twisting of Annorax's good intentions is what really caused this mess to begin with.
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 permenant 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, bruying such dangerous knowledge.
And The ancient artifact that they got their knowledge from and their civilization has been guided by is revealed in the end as the same "species" as the Guardian of Forever.