I forgot to mention, that ending bit with VOY being attacked by the Kazon was the middle of Season 2 and not the finale.
Second half of Season Two
The next episode would open up with the huge explosion having come from the Kazon Carrier, as several Vidiian Cruisers show up and open fire on the Kazon force.
They destroy Cullah's ship, killing him. But I'd leave it ambiguous as to whether or not Seska got out alive.
The rest of the Kazon forces break off the attack and retreat back to the Periphery while the Vidiian ships pick up the VOY escape pods and tractor the ship away from the battlefield to Vidiian space, along with the Talaxian fighters.
The pods are put in the same large cargo area and the crew exit, ready to fight to the death rather than be harvested, when a figure appears and tells them that it's alright, they will all live nice healthy long lives.
The Vidiian crewmembers all come to Voyager crew and thank them for ridding them of the Phage. Chakotay explains that the B'Ellanas found out that since weren’t meant to last and their bodies were falling apart they decided to use what time they had left to help Voyager. They asked to be given back to the Vidiians so they could create a cure for the Phage from them. This would then make them grateful enough to ally with VOY and give them the major allies they needed at that point (as the League was turning out to be a dead end).
Janeway (who was recovered from the ruined bridge of Voyager) would wake up to Chakotay and Tuvok in a Vidiian med-bay, where Chakotay would explain everything to her.
The Vidiians now have the cure and have taken VOY to a Vidiian outpost to repair it. It will take time so the crew can rest and recover. A lot of them need it, especially the ones who are rather taken back at the idea of the Vidiians being their allies now.
Fortunately, Denara Pel is there to serve as the Vidiian liaison to the crew, so they can at least trust her.
Time would pass, with Neelix seeing how worshipful the Vidiians now are acting towards the VOY crew, and how they talk about how they can finally return to their older ways of being "teachers and scientists" and stuff, like they were millennia ago. But others are more depressed, wondering how they can make up for what they've been doing, who would stand up for them or believe them? One ship full of unknown aliens isn't enough.
Neelix would then come up to the Vidiian Commander of the base and offer a proposal to them.
Janeway would be going over some repairs/upgrades the ship is getting from the Vidiians, when a Vidiian diplomat would come to her and tell her what a wonderful idea she proposed and how it will be the old age of greatness again.
Janeway would wonder what this guy is talking about, and is stunned when she finds out:
Neelix told the Vidiians that if they want their old reputation, or anyone willing to stand up for them, they could give a good message by liberating the Talaxians from the Haakonian Occupation as the Talaxians were a well-liked people with a reputation for honesty. The Vidiians are already assembling a military force to begin the campaign if the Haakonians refuse to withdraw via diplomacy.
Moreso, the Vidiians returning to the old ways and with allies can recreate the "Conclave", an interstellar alliance of worlds that once existed millennia ago but came to an end when the Vidiians (who were the primary proponents of the original Conclave) were infected with the Phage and the Conclave was all but destroyed in the "conflict" 2000 years ago that left most of the members of the Conclave extinct and their worlds ruined.
It turns out that what is now known as the Periphery was once a rich area teeming with intelligent life, but the "great war" left it all virtually destroyed and the life extinct, with the surviving races in what is now the Central Core joining into the League of Spacefaring Civilizations. This is the origin of the ruins and devastated worlds VOY encountered on their way through the Periphery.
Janeway is understandable furious when she realizes who suggested this idea to the Vidiians, claiming the VOY crew were the ones who originated the idea. Confronting Neelix is a scene similar to the Sisko-Garak confrontation at the end of "Pale Moonlight" she accuses him of exploiting the Vidiians for his own ends.
He counters that what he's done is best for everyone involved. The Talaxians will be free and will be more than willing to join this new "Conclave" the Vidiians want to create as to gain a powerful military ally (the Talaxians however will still see the Vidiians as organ harvesters, and when they liberate Talax they'll just think Neelix went nuts and sold them all out in mass-harvest so at first the Talax rebels will fight against the Vidiian and VOY forces), and their PR skills will be enough to convince other powers in the Periphery to join. VOY will have helped to stabilize what was a chaotic, disjointed region.
And he states he also did it for VOY as well, because "Since you can't go home, you can bring home here". He's been studying their "Federation" and while he finds some of it to be left wanting, he thinks it's a good basic idea. Janeway shoots back that the Federation’s values are something she and the crew worked hard to preserve, and it got them this far. Neelix should know better than to just discard them right in her face. Neelix then apologizes and admits that maybe there is such a thing as too much cynicism.
Janeway reluctantly agrees with Neelix, after even Tuvok (it's logical) and Chakotay (it helps people and give VOY all the allies they'll ever need) also side with him.
But as punishment, she makes Neelix the VOY Ambassador to the Vidiians, so he has to spend all his time around the guys who took his lungs.
The History of the Conclave’s Fall
The "Great War" that caused the Vidiians to be infected with the Phage, made the Conclave fall apart and destroyed all the life that existed in the Periphery was against the Fluidics when they first entered this dimension from a huge Fluidic Rift that closed soon after they arrived.
They fought a war against the alien races of the region 2000 years ago, using their bio-infection (that thing they did where if you get punched or slashed by them their DNA enters you and eats you alive), their telepathic powers and their vast bio-weapon power to destroy planets and entire species, with the Conclave and other powers desperately fighting for their lives.
There was another major power around, the mysterious and isolationist Voth, and it was their aid in the war that beat back and held off the Fluidics for the most part. But they took so much loss of life and damage in the war they removed themselves from the Galactic Public in all ways and practically disappeared after the war, no one having seen them since.
The Conclave's best minds were able to come up with a bio-weapon that halted the Fluidic advance and killed many of them, but not before the Vidiians themselves were infected with Fluidic DNA. They tried using their advanced medical tech to stop it, but instead they caused the Fluidic DNA to mutate into the Phage, which then spread to their entire race and turned the Vidiians into the desperate organ-hunters they were in the beginning of VOY. The Conclave's knowledge was lost to time and so was the bio-weapon they used.
The few surviving Fluidics then retreated and have spent the last 2000 years rebuilding their species and their forces for another war, with the League of Spacefaring Civilizations preparing for their return.
Also, due to the Fluidics' destructive usage of telepathy in the Fluidic Wars, this is what caused the Devore Empire to be so anti-telepathic and develop anti-telepathy technologies.