Alt Trek/Fanfic

I'd re-do ST: Voyager by having the crew exile Janeway after the episodes "Scorpion" and "Tuvix" instead of allowing her to execute the composite 'Tuvix' character . This puts the remaining crew in conflict with the Borg* and a renegade starship captain, but not after the ship itself "mutinies".

A secret AI programme takes over the vessel, leaving Tom and Harry left in charge as the only original Starfleet officers remaining. They "speed" ** to reaquire Janeway but Borg advancements to Voyager make them a target for an unexpected enemy: captain Ransom of the Equinox, who was also stranded in the Delta Quadrant with his crew but is prepared to disregard Federation morals and his own training in order to return home.

Believing Voyager to be some variant on the Borg Sphere-design Ransom has his crew intercept Voyager. Still being Starfleet, Ransom is recognised as so by the mutinous AI and grants him access to the ship's systems. Harry Kim and Chakotay secretly leave in the Delta Flyer to retrieve Janeway for the final confrontation with Ransom.

*I can't remember what the Borg in particular had to do with this particular scenario, other than hypothesising that Torres and Seven really ought to have come up with a working cloaking device to hide Voyager from the Borg. Perhaps the only reason this didn't actually happen is because Janeway wouldn't violate the treaty which bars Starfleet from producing a cloaking device of their own.

**I can't think of a way to re-word this sentence, hence the quotations.

Update 22.5.2017

A combination with Deep Space Nine could result after the Voyager crew return to the Federation. Captain Tuvok, Janeway being demoted by the crew to Lieutenant Commander, being the only suitable replacement for Janeway makes contact with the Romulans via the Ancient Communication Network (used by the Hirogen). The ACN is used to beam the Voyager crew to a deep-range Romulan explorer ship. Voyager itself is left under the command of the covert AI system, possibly with Janeway and Ransom remaining as semi-prisoners, and ordered to warp to the next ACN nexus.   

The crew discover that (obviously events on DS9 are altered) the Federation, the Cardassian Union and the Tholians made a peace deal with the Dominion. Sisko and the Bajorans rejected this and made an alliance with the Klingon Empire in defiance of orders. Vulcan left the Federation and revived peace talks with the Romulans. They also started providing covert aid to the Maquis. Tuvok, Sisko and others agree on a plan to destroy the Dominion without starting a war in the Alpha Quadrant: they will take the Defiant into Borg space and provoke the Borg into following them into Dominion space. The Dominion would be too distracted trying to fight the Borg to be concerned with conquering the Federation and the Borg would waste resources trying to conquer the Dominion. 

Second update 2.6.2017

I ought to point out that Tuvok and Sisko can travel between the Delta and Gamma Quadrants via the Barzan Wormhole, to Voyager via the ACN nexus and to the Gamma Quadrant via the Bajoran Wormhole.