Alternate Voyager Endgame Idea:
Voyager discovers an advanced organisation with an enormous empire and advanced technology. This organisation (The Confederacy, similar to the Federation) has discovered the Borg Transwarp hub and want to take it down. They have never been assimilated by the Borg and thus the Borg have never gained knowledge about their technology and are reluctant to put ships and their people on the line to attack the hub. First contact with Voyager presents them with an opportunity to attack the Borg and bring down the Hub without putting their own people on the line.
The Confederacy presents Voyager with a deal. Voyager will be outfitted with the necessary technology to take down the hub and in exchange one of their ships will Tractor Voyager to the Alpha Quadrant, a journey that would only take a month.
Janeway says no but after asking the opinion of her senior officers they decide to give it a try, a chance to not only get home but deliver a crippling blow to the Borg.
Voyager is outfitted with ablative armour generators and transphasic torpedoes.
In the nebula Voyager manages to battle its way to the hub taking down as many as 7 Borg Cubes. When they reach the hub however it's made clear that Voyager is not equipped to pull off the job and it would require an entire fleet, they fall back to the Confederacy and Janeway attempts to persuade them to make an all out attack on the hub.
The Confederacy refuses but Seven of Nine manages to change their mind. She tells them that their technology is superior to the Borg and it would be advisable to hit the Borg now rather than sit and wait for the Borg to come. With the hub in place the entire Galaxy will fall to the Borg.
The new plan is hatched that the Confederacy will attack the Hub whilst Voyager infiltrates unimatrix zero using a Confederate cloaking device and infects the Queen with a pathogen to bring down the hubs defences.
All seems to be going to plan until Voyager is detected whilst under cloak, Voyager is caught in a Borg tractor beam before they can decloak and deploy armour. Borg drones begin beaming to Voyager and an internal ship battle commences.
Seven of Nine realises that to get the pathogen released a person will need to carry it and the Queen must assimilate them. Going against orders she escapes the ship in a shuttle craft and heads for the Borg Queens unicomplex, before she reaches the complex she is beamed directly to the Queens location.
Seven tells the Queen that she will freely return to the collective if the Queen allows Voyager to leave. The Queen refuses and proceeds to inject Seven with nano probes. The pathogen is instantly released into the Queen and she begins to lose contact with the collective, drones begin to malfunction and the Voyager crew manage to repel the Borg invasion force with no casulties.
The pathogen however does not work as initially intended. Instead of only cutting off the Queen from the collective the queens nanoprobes in Seven along with the pathogen within seven begins to connect Seven into the hive mind in place of the queen.
The Confederacy meanwhile manage to taken down the hub.
The Queen falls to pieces leaving Seven of Nine in full control of the Borg Collective.
Seven of Nine becomes the new Borg Queen.
She contacts Voyager and tells Janeway that a Borg cube will be dropping by shortly to take her and the crew back to Earth.
before Janeway can say anything Seven of Nine thanks Janeway for her help all the years but says she does not know where she is to go from here and cuts off the transmission.
A Borg cube tractors Voyager to the Alpha Quadrant and then leaves back to the Delta Quadrant.
The future of the Borg is unclear but Voyager is finally home.
