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After Sam chose to leave the family and hunting and attend Stanford, John cut off contact with him, although he regularly visited Palo Alto to check up on him.<ref>[[1.08 Bugs]]</ref> John and Dean continued hunting together, with Dean also going on hunts on his own as he got older. Around this time John and Bobby had a falling out -- Dean comments that the last time Bobby saw John he nearly "filled him with buckshot."<ref name="one22">[[1.22 Devil's Trap]]</ref>
In 2003, John ends up in 2019 after Dean uses a [[Baozhu]] to grant "what his heart desires," - hoping it will rid remove [[Michael]] , who is trapped in his mind. John gets a chance to reunite with Mary, and reconcile with Sam and Dean. However John being in 2019 is tampering with the timeline, so they destroy the which pearl and send John back to 2003, where he wakes with no memory of what has happened. <ref>[[14.13 Lebanon]]</ref>
In 2005, John got a lead on the [[demon]] that was responsible for Mary's death, and he left Dean in order to pursue it. He tried to keep both Sam and Dean at a distance in order to protect them, even refusing to respond when Dean called him when he and Sam returned to Lawrence in response to Sam's visions<ref>[[1.09 Home]]</ref> or when Sam called to tell him Dean was dying.<ref>[[1.12 Faith]]</ref>
