She was saved from a fatal car accident by the Valeyard and became his companion. She helped him to prevent his meeting with Mel Bush and took her place in the Sixth Doctor's timeline, accompanying the Valeyard to the Hyperion III in an altered version of the events that the Sixth Doctor and Mel had experienced.
By the time she met the alternate Mel, she had been travelling with the Valeyard for some time. She insisted on calling him "the Doctor", and was confused about his intentions when he began meddling with history and talking of conquering and destroying planets. She seemed to have been somewhat desensitised to violence, but later helped him when he accidentally killed two previous Doctors and was suffering the effects of a grandfather paradox. She showed herself to be quite clever by working out what went wrong and suggesting looking for a solution in the Doctor's diaries.
Although Ellie appeared to trust the Valeyard, he stabbed her to death with a switchblade knife to prove to Mel Bush that he was no longer the Doctor, and saying he wanted to be alone. He may have later regretted her death, referring hesitantly to having "allowed her to die". (AUDIO: He Jests at Scars...)