In Source Code (2011), At the beginning of the movie, Capt. Stevens looks in the train bathroom mirror and sees Sean Fentress, a teacher, who's identity he has been assigned within the Source Code. However, to himself, he still appears to be Capt. Coulter Stevens, due to his physical mind projecting himself into his Source Code consciousness.
In his last "mission" into the Source Code, Capt. Stevens successfully established an alternate timeline. There is a brief scene at the end, showing him and Christina in front of Cloud Gate. As the camera pans away, the viewer can see that Capt. Steven's reflection shows that of Sean Fentress, as it did in the train. However, in the final scene, Capt. Goodwin is shown looking at Stevens' mutilated body, indicating that Stevens still exists as an Air Force officer in the alternate timeline. If Stevens truly created an alternate history in which he is Sean Fentress, why are his appearance and reflection still at odds? He is no longer "plugged in", and in a real sense no longer has any connection to the Stevens in the new timeline (who is back in the facility). At that point, Stevens' consciousness is back at the lab in his body. Fentress is not Stevens-in-Fentress, he's just Fentress.