She left him
Rose still couldn't believe it, it had been almost two years since she last saw the Doctor. When Rose last saw the Doctor he was talking to Jack outside the TARDIS after they had saved the universe, When she looked at him (well the back of him) she knew that she would never have a goodbye or here those words she had long to hear.
Flashback
"I can't find him or the metacrisis, please where are they old girl." Rose could tell the TARDIS hesitated briefly but showed her the way to the library.
Rose was just about to go in when she heard
"When we go back to Pete's World, I am leaving you and Rose there" the brown suited Doctor stated
"Why would you do that? Do you actually really believe that is going to work?" The blue suited Doctor asked
The brown Suited Doctor looked the metacrisis and stated "it has to work because I can't let her give up her family and life for me, she is human, she will wither and die, she deserves to have a happy and normal life."
"Ok what the plan" asked the blue suited Doctor
Hearing those words Rose couldn't believe that he would do this to her or to himself. He wasn't even giving them a chance. So Rose came up with her own plan, she wasn't going to sit by and let him dictate her life.
Rose went back to the control room where she pulled Jack aside and asked for his help, and not to repeat anything to anyone else. Jack gave her his vortex manipulator and set in the coordinates to meet him at, on the condition that she tells him everything when she gets there. She agrees and he seals it with a kiss.
Rose then goes to her mother and tells her goodbye, that when the TARDIS lands she will be leaving, Jackie knew that she had to let her go.
As the TARDIS landed the Doctor in the brown suit went outside to saying goodbye to Sarah Jane, Martha, Jack and even Mickey, while the blue suited Doctor was talking to Donna, Rose was able to sneak out of the TARDIS and start her life.
End Flashback
After Rose left the TARDIS, she met up with Jack and explained about how she heard the Doctor tell his metacrisis how he was going to leave them behind in the parallel universe, and how that universe was slowly killing her. Jack gave her a job, and from that moment on Rose started her new life, without the Doctor.
