So the Voth City-Ship has de-cloaked (their cloak is much more powerful and totally inviisble to all of VOY's scans) and in exchange for VOY coming with them they won't open fire on the Conclave HQ and all the representatives housed in it.
VOY is then swallowed up inside the massive vessel and taken somewhere while the crew are given restricted access to the ship. They notice that much of the design seems similar to League technology even though the Voth have not been seen for 2,000 years.
A Voth scientist (his name was Quarren, right?) who states he is an anthropologist greets the crew. He's been wanting to study the Federation people for some time now but it took the growing situation with the Borg and the return of the Fluidics to convince his people to finally do so.
He decides to answer some questions in return for their cooperation, but this is mere courtesy since the Voth could just take over the ship, strip it of all knowledge they seek and tear whatever personal information is needed from their minds.
He explains that this one massive vessel is all that's left of the Voth people and that a side-effect of the usage of bioweaponry in the Fluidic Wars left it hard for them to reproduce, some side effect near-sterilizing their DNA. But since they all live for so long they didn't die off long ago. Their elders are contemporaries of the First Fluidic Wars.
As for why they only took a direct interest now when they showed no interest in galactic affairs before? They DID have an interest: The Voth shows them a timeline of the League's existence and VOY notices that times of expansion are around the same time the Voth claim they would show up to observe how the Deep-Beta region was recovering from the Fluidics. The Voth in fact created the League from nothing by periodically advancing their technology and giving advice/motivation to the League leaders so they could act as the Voth's proxy/front while they remained safe on their City-Ship.
But now with things reaching a critical point they feel they must take a more direct hand in this second Fluidic Invasion.
They appear at the League capital world where they are informed that the League succeeded in capturing and holding a Fluidic separated from its people and its craft without it committing suicide. It's now at a lab and they want to test out VOY's nano-weapons on it to see if they themselves can improve on them.
The lab as it turns out is very low-tech in most regards, to keep the Fluidic from being able to escape if it did break out of the containment area (one of the only advanced parts).
When VOY does get there they get no response from the Lab. After being told this is part of procedure to keep the lab a secret Janeway decides to go down there herself with the nanoweapon data because she doesn't want to risk anyone else's life. But to insure that she will keep her end of the bargain the entire bridge crew are sent down there by the Voth so she will have to worry about others' lives.
The Fluidic has escaped and it killed the guards and trashed the most advanced parts of the lab. All that's left are the run-down parts of the place (it used to be a refinery).
The surviving scientists and the crew come up with a plan to fight back: The Fluidics' mental powers have been dampened by drugs it was exposed to on arrival but it still has awesome physical strength so they have to find a way of trapping it again. There are parts of the old Refinery that can be sealed off so it can't get out (the doors are too thick for physical strength to break) and they plan to try and use their weapons to ignite refinery gas and cause a big enough blast it will physically blow the Fluidic creature towards the part of the tunnel system where it can be trapped.
The get to work setting it all up when the Fluidic attacks them prematurely, and one guy fires his phaser while being assaulted which sets off the blast. It forces everyone including the Fluidic to the end area where the door can be sealed, but the Fluidic still isn't inside the area yet.
Tom, seeing they have a chance now (and he'd have been rather depressed for a while since everyone he became close to has died or left him like Harry B'Ellana and Seven) runs into the chamber and gets the Fluidic to follow him. This sets off the motion device that triggers the door close while its' killing Tom. It's trapped but Tom is dead.
After the League sends in another battalion of troopers and engineers to get the place fixed up, the Voth demand that VOY use their nanotech weapons in experiments on the Fluidic. Kes then tells everyone to stop and realizes she can communicate with the Fluidic, it's still weakened mentally but can now communicate. It's weary of fighting and killing and saw enough inside Paris' mind to know when it's beat.
It agrees to communication and when everyone demands what the Fluidics' intentions are and why they have been so hostile for 2000 years it responds that its people are prisoners in this dimension and have been since they were pulled here 2000 years ago by the Controller who refused to let them leave until they had destroyed everything in the Galaxy because the inhabitants wanted a challenge. All attempts at communicating before failed and war broke out due to these failures to communicate, leading everyone to where they are now.
When Kes asks about the Controller, what she sees is too much for her mind to comprehend but she realizes it is very familiar.
Correlating all their data on powerful beings in the Deep-Beta Quadrant that had been around for the last 2000 years a list is done up when Kes realizes what she saw in her mind and cross-references it with the data.
She brings up how the Caretaker and his mate arrived here 2000 years ago and how while the Caretaker remained to care for the Ocampa his mate left for other pursuits. Now they know what happened to her and what that pursuit was.
The "Controller" is the female Caretaker, and everyone that had happened in the last 2000 years has all been her grand experiment.
