An Old Enemy
Working together the Vidiians, the VOY crew, the Talaxians, the Vaadwaur and the Krenim are able to re-create an ancient FTL Engine the old Conclave had that was able to move much faster than any current Warp Drive or even the League's FTL.
This new drive (Quantum Slipstream) is powered by resources found in the Periphery (not available in the Alpha Quadrant) and the one prototype they build begins testing for use on Voyager. With Denara Pel assembling a Conclave delegation they prepare to leave for Known Space to let Starfleet know about all that they've encountered as soon as the QSS is ready.
However, before they can go a major complication arises.
We cut to a Talaxian merchant ship/mining ship just minding its own business, the Captain has a pet that's a counterpart to a dog, etc, when a large object would appear on their scanners emerging from some kind of unknown rift near the ship, throwing it out of control.
VOY would pick up the automated distress beacon and send an away team to investigate.
Harry would be looking around in one area and find evidence of a fight with energy weapons, but no signs of disintegrated bodies on the Vidiian scanners (they use those now instead of Tricorders) and then locates one member of the crew at the communications, except he's dead. He looks like he was mauled by some vicious animal.
He would then go deeper and see several other crew members who have all been killed in the same way, and several of them look like they were fighting something when they died. He doesn't realize there's something in the chamber with him, and it seems to have extra "bits" on it that are artificial.
He then finds one sole surviving Talaxian who locked himself in a locker to survive, but he's in severe shock. As he calls the medical team on his communicator, Harry hears a growl and turns around just in time to barely dodge a tackle by the Captain's pet, which has been turned into a vicious killer. It has robotic enhancements and shoots tubules out of its mouth. It finally gets him pinned down, but before it can rip him up the Talaxian picks up Kim's phaser and kills the thing.
The survivor then tells the rescue team that a humongous vessel appeared out of no where and knocked their ship out of control before it beamed 2 of its crew onto the mining ship. They transported several of the mining crew away, but the remaining crew fought back and killed one of them with their weapons, but somehow the second one was unaffected by them (adaptative shield) but the Pet attacked and killed the other one with its' teeth and claws. Before it died the alien injected the pet with something that mutated it into a bio-mechanical monster; it then slaughtered the rest of the crew except him since he hid himself.
He'd show them the corpse of the alien the pet killed before it mutated: It's a Borg.
We'd open with the same teaser: A Borg ship (in this case, a Sphere) would contact some unknown force, and we'd see the Borg Sphere being blasted apart by it.
VOY realizes the huge ship must've been a Borg Cube, and the rift it emerged from was a Transwarp Conduit like the ones Lore’s Borg used in “Descent”.
VOY and the Conclave then contact the League and give them their information on the Borg in hopes to mobilize all the major forces. The League then begins sending out patrols to investigate these new intruders.
VOY would go searching when they receive information from League Sensor Outposts. It’s very tense, like in "Descent" where the ENT-D was always monitoring for Borg activity.
Eventually they find something, and not only is it a Borg signature, they read something else that the League Computer Servers they're interfacing with can identify when VOY's own computers cannot: Fluidic
They arrive and find the same Borg Sphere from the teaser partially destroyed and maybe one or two dead Fluidic Bio-Ships as well. The League sends a battalion of troopers onboard the Sphere and VOY sends its own team to investigate on a shuttle.
This is mainly the same as what happened in VOY, where they encounter a Fluidic soldier, Harry gets infected, etc.
They leave, but someone else had crawled onboard their shuttle, a female Borg.
She reveals herself and tries to assimilate them as the shuttle leaves the Borg ship, but at the same time a group of Borg corner the Fluidic on the Sphere and assimilate it; As it is assimilated it lets out a psychic "scream" that overloads the Borg it is now connected to which causes a massive "system crash" that terminates the Collective onboard the Sphere. The female Borg is far enough away on the shuttle that she doesn't die but her connection to the Borg is weakened.
She tells them she is Seven of Nine and as she is alone and outnumbered/outgunned she will not harm them. When asked about what the Borg are doing in this area of the galaxy she informs them that the Borg recently picked up energy emissions from this part of the Beta Quadrant that interested them, so they sent a scout force to investigate.
(The emissions are the energies the Fluidics gave off in the Fluidic Wars 2000 years ago, it just took that long for the energy emissions to naturally make it far enough to be picked up by a Borg ship)
The VOY crew figure out from what information the League and Old Conclave records have on the Fluidics that they are all powerful telepaths (explaining the anti-telepathic stance of the Devore Empire) that have their own form of a Collective although each Fluidic is an individual unto themselves. When the Borg tried to assimilate one of them the Fluidic's own telepathic mind reacted badly to being forcibly grafted to the Collective, and "self-destructed", but since it was linked to the immediate Borg when it died the psychic shock went into them as well and killed them all.
So it seems that being assimilated causes Mutually Assured Destruction for the Fluidics and Borg, and since the Borg can't assimilate them they intend to now destroy them.
Thus the season ends on the prospect of an all-out war between the Borg and the Fluidics, with the Deep-Beta Quadrant as the battlefield.