|“||No, me and Sam, we hadn't talked in... hell, five years.||”|
After an encounter with the Horseman War, Dean decides that he can't trust Sam anymore and the two go their separate ways. After encountering Lucifer in his dreams and learning that he is the true vessel of Lucifer, Sam attempts to reconcile with Dean who refuses.
Dean and Sam never reconcile and Sam eventually says "yes" to Lucifer in Detroit, becoming his vessel. With Sam as Lucifer's vessel, the Apocalypse went into full force with the angels abandoning humanity and the Croatoan Virus being let loose on Earth.
In 2014, the Dean from 2009 is brought to the post-apocalyptic future by Zachariah. When the two Deans meet, the future Dean lies that Sam died in a heavyweight showdown in Detroit, admitting that he hadn't talked to Sam in five years.
Later, before going after Lucifer with the Colt, the future Dean admits to the 2009 Dean that Sam didn't die but instead said "yes" to Lucifer in Detroit. Dean admits to his past self that he doesn't know why Sam said "yes," but feels that they have no choice but to kill him in order to kill Lucifer and save what's left of the world. To prevent it from happening in the 2009 Dean's time, the 2014 Dean pushes his past self to say "yes" to Michael once he is returned to his own time.
During the attempt to kill Lucifer, the 2009 Dean meets the 2014 Lucifer in the body of this Sam. While talking with Dean, Lucifer acknowledges that it must be hard for Dean to see him in Sam's body and repeats what his present day self told Sam that it always had to be Sam that was his vessel.
After being returned to 2009 by Zachariah, Dean decides not to say "yes" but to instead reunite with Sam, having learned from what he saw of his future self and the future Sam that they were stronger together.
- This Sam shares the same history with the Main Universe Sam Winchester until the beginning of the Season 5 episode The End when Dean refuses to reunite with him.