I read a fanfic a while back that I liked, and now I can't remember where I read it so I'm hoping you can help me out... 
It's about Janeway discovering that Chakotay has made a program on the holodeck of their house on New Earth and also a hologram of her. So she starts to replace the hologram with herself and then she ends up pregnant and has to tell Chakotay the truth.

It's about Janeway discovering that Chakotay has made a program on the holodeck of their house on New Earth and also a hologram of her. So she starts to replace the hologram with herself and then she ends up pregnant and has to tell Chakotay the truth.