Doctor Who secretly rewrote Rose and Donna's fates. When Doctor Who returned in 2005, showrunner Russell T. Davies chose to take a slightly different approach. While the Doctor was undoubtedly the star of the show, Davies understood his (or her) companions were an essential part of the story too. They offer an interpretative lens through which the viewer sees the Doctor, helping audiences to understand the thoughts and ways of the enigmatic being.
Played by Billie Piper, Rose was the first companion of the relaunched series. An ordinary working class girl who soon proved her courage, Rose fell in love with the Doctor. That love led her straight into the firing line when Daleks and Cybermen went to war, and she ultimately found a home on a parallel universe - one where she actually fell in love with a duplicate of the Doctor. Donna Noble, played by Catherine Tate, was another of the greatest companions of the Russell T. Davies era, and she too fell foul of the Daleks. Unlike Rose, Donna went back to ordinary life, her memory wiped because her mind could not bear the strain of the knowledge she had absorbed in order to defeat the Daleks.
But Doctor Who has secretly rewritten Rose and Donna's stories. In Doctor Who season 5, the newly-regenerated Eleventh Doctor learned humanity had forgotten the various Dalek invasions. He learned this was because history had been rewritten, the result of a second Big Bang caused by his own exploding TARDIS. The Doctor never really stopped to think what this meant in terms of the overall timeline.
The Daleks previously invaded Earth in the Doctor Who season 2 episodes "Army of Ghost" and "Doomsday," and the season 4 episodes "The Stolen Earth" and "Journey's End." These events have been wiped from history, meaning everything that happened to Rose and Donna - including Rose's becoming trapped in another universe, and Donna being forced to absorb the memories of the Doctor in order to stop the Daleks - has been erased from the timeline as well. Presumably both women left the Doctor for different reasons in this new timeline - reasons that have never been shown.
Doctor Who's continuity has always been confusing, with the timeline in a constant state of flux - explaining why there have been no less than three different tales accounting for the destruction of Atlantis. But this is one of the most intriguing changes to continuity of all, with the Doctor's own past rewritten, and the fates of two of his most popular companions adjusted. It will be fascinating to see whether Doctor Who ever addresses this directly.