Star Trek: Endgame Fiction Vs. Reality

What Happens In The Episode:

Although Chakotay would make it back to the Alpha Quadrant in Admiral Janeway's original timeline, the extra time aboard Voyager would prove to be his undoing.

The furtive romance between Chakotay and Seven of Nine during the show's later seasons would blossom into a love strong enough to result in marriage. Tragically, three years after the events of Endgame, Seven would meet her end in an away mission and die in her husband's arms. Although he lives on, he's never the same again, and Janeway theorises that his death on the year of their return is one of grief.

What Really Happens:

To the delight of fans, and likely also Jeri Ryan and Robert Beltran, Chakotay and Seven's relationship would not stay the course on their return. Whilst Seven would leave Starfleet to join the Fenris Rangers, Chakotay stays the course and captains the USS Protostar, bizarrely delving right back into the Delta Quadrant after so long getting out of it - hey, if I'm stuck somewhere for seven years, I'm taking a bit of a long holiday from it.

Aided by a hologram of Captain Janeway, Chakotay's ship is flung decades into the future by a temporal anomaly, encountering the Vau N'Akat, before returning without its captain, but with its hologram, to set up the events of Star Trek: Prodigy.