Star Trek: Voyager AU with divergence points at S2E25: Resolutions, and S3E5: False Profits
A plasma storm comes through only three weeks into their stay on New Earth, leaving Janeway without any means to continue her research, and she and Chakotay have a longer wait for Tuvok to return with a cure. In that time, they become closer, and get in the habit of sleeping in the same bed. (How often that means there’s more than just sleeping, I leave to the reader’s imagination.)
Two months later, Voyager is pulled into the destabilizing Barzan wormhole along with the Ferengi, and are spat out at one of the former terminus points, past the Denkiri Arm in the Gamma Quadrant, putting Voyager a century from home at warp 9, and an unknown distance from the Idran system and the wormhole that would get them to Deep Space Nine in a fraction of the time. (Fortunately for the Ferengi, they’re not deposited at the same place as Voyager.)
Janeway is faced with two major decisions, finding she is pregnant (the virus she and Chakotay had been infected with on New Earth interfered with both of their birth control), and she must choose how to deal with that, as well as making the decision on how to get Voyager home.
There's a Mirror on the Wall 