Because the Conduit was incomplete and unstable, Equinox and Voyager emerge in different areas of the Delta Quadrant.
In this version, the DQ is very much a wasteland with nothing but Borg-scarred worlds and refugee fleets of survivors who survive mainly because their ships and technology are less advanced than the tech already assimilated by the Borg when their worlds were first attacked. The Borg pretty much see them as less than nothing and leave them alone. Seven comments that the Borg may just be leaving them alone in the idea that they will inhabit some new world and the multiple survivor races will work together to create new technologies and ideas that the Borg can them come in and assimilate.
IE, it's a Borg breeding program with no one realizing it.
After going around looking for Ransom and trying to co-relate any data they got on the unstable Conduit with other DQ survivors to perhaps try and stabilize it or make their own to return to known space, VOY learns that there is at least one Civilization, the Arturians, that has survived thus far and heads there to see if they know anything.
Turns out they've survived for two reasons: They hunt down individual ships of advanced races and set them up for the Borg to take them so they'll leave them alone, and they form conscript fleets of unwilling alien races to defend themselves from Borg attacks so anything the Borg assimilate is from those other races and not from the Arturians, meaning if they're interested they go after those races and not the Arturians who conscripted them in the first place.
The greater of two evils
VOY and Equinox both find themselves reluctantly conscripted into a massive armada put together to defend from a Borg Cube that has finally decided to investigate one of the Arturian's own planets, meaning if they fail the Arturians are doomed. Thus lays the moral quandary: the normal populace are unaware of what their army has been doing and are innocent. If the armada fails they will all be assimilated once the Borg decide to really attack the Arturians. But they cannot ignore how the Arturians had been sacrificing others to save themselves.
They don't have time to fully answer these questions as the Borg attack and they are forced into the fight. They do manage to do enough damage with their various different weapons (Borg can't adapt to all of them at the same time) but upon its defeat (and the destruction of 1/4 the armada) the Cube just leaves rather than fight to the end, much to everyone's puzzlement.
Equinox has been critically damaged, and its crew are transferred to Voyager, since to the Arturians they can work together, being the same organization. This leads to conflict between the crews, especially between Ransom and Janeway who is disgusted with how Ransom is trying to act paternal to Seven.
More conscript ships are arriving to reinforce the fleet in case the Borg return, and Ransom tries to convince Janeway to just abandon the conscripts and take them back to the Deep-Beta Quadrant through the unstable Conduit, since he's combined their data with his and he knows how to stabilize it and enter it. Janeway is unsure since stabilizing it leaves the possibility of the Borg themselves using this new conduit, and she doesn't want to abandon the other conscripts.
Meanwhile, Seven keeps having Borg related nightmares, but doesn't know what they mean.
Before they can reach an agreement, the Cube returns, but with friends. Other Cubes are there as well and they all combine together to form a Massive Fusion Cube (8 cubes together).
The whole time this was a Borg trick, to send in one Cube to learn while testing out their new Fusion Cube as a weapon (possibly against future battles with the Fluidics).
The battle is a slaughter, and when things are looking bleakest the conscripts receive a transmission that unlocks all the controls the Arturians had put on their ships and an armada several times the size of the conscripts arrives, entirely made of Arturian vessels.
They have decided that the Fusion Cube cannot be stopped by the conscripts and rather than have them all die they are released, while the Arturians will use their advanced weaponry for the first time to fight the Borg. Janeway finally makes her decision to leave and head for the unstable Conduit.
As they leave, Seven comes to Janeway to tell her she's deciphered her dreams: she'd unwittingly been overhearing the Collective through some leftover Borg tech in her brain. They scanned that VOY was a Fed ship and were wondering how they got to the DQ and to that end had sent a second Borg vessel after them, a Tactical Sphere (not the smaller FC one).
They get shot enough to damage the shields and Seven is beamed onto the Borg vessel and re-assimilated while VOY is using Ransom's equations to stabilize the Conduit, it works but the conduit is shrinking. They got through with the hope that the Sphere will follow them and they can get Seven back, but instead the sphere hits them with a tractor beam while they've just entered the conduit and is dragging them back.
But, as it turns out Seven's time away from the Collective had given her enough independence combined with her knowledge of the Borg to perform a miracle: she is able to influence the Collective on the Sphere for 1 second. But 1 second is all she needs.
She orders the ship closer to the Conduit, which is now too small for it to fit through. It collides and combines with the Conduit which cancels both out, destroying the Sphere and the Conduit. VOY survives due to Seven's sacrifice.
Ransom then breaks down and admits what a poor father and Captain he was, and puts himself in Janeway's custody.
The final image of Ransom in this series shows him in a Jail Cell holding two photographs: one of his family (his wife and young daughter Annika), and one of Annika's adult borg self, Seven of Nine.