Take one of a dozen failed attempts to get back to the Alpha Quadrant, and you have the potential for Janeway's ship falling into a black hole and coming out were the Prime Universe's Voyager 6 ended up. Janeway's crew is perhaps killed by radiation and the machines try to figure out USS Voyager from the computers. Probably mash up some things from the main computer, captain's log and other entry (perhaps even have issue with the Doctor and 7of9's remaining Borg bits.) And simply build a better ship around the crippled Voyager to fulfill its two goals. The ship was built as an explorer, so it would follow the Starfleet motto to seek out new live forms and all that...but also follow Janeway's mission...to get back home. (If Katie is hot stuff now, imagine V'ger using her image in place of the Doctor's to communicate instead of Ilia.
Because things are not equal, V'ger N'656 heads for home...at the wrong time and in the wrong universe. Stuff happens and by the time it gets to Klingon Space, it has the massive cloud for reasons. Its weapons, regardless of it they are upgraded by the machine race, would easily be 100 years better than anything the Klingons or Starfleet has. Remember what USS Defiant NCC-1764 could do to NX-01 era ships. Now image the same thing happening from USS Voyager to the Constitution era.
Depending on just what tech difference the new films have verses a Prime Universe Voyager remade for a new film V'Ger.