As revealed by showrunner Scott M. Gimple on the "Walking Dead" Season 6 Blu-ray commentary, Morgan was going to appear in the train car with Rick and the other prisoners of Terminus during the fourth season's finale.
"At the end of [the episode], Rick would say, 'They're screwing with the wrong people,'" said Gimple during the commentary for the episode "Here's Not Here," "and a gentleman would come out of the shadows of the train car and he would say, 'Yeah, they are.' And that would be Lennie, as Morgan. And it looked like it almost could have happened."
Unfortunately, James' scheduling on another show prevented them from realizing the sequence, but it sounds like Gimple wasn't too upset by the turn of events.
"[It] allowed us to do something super cool, which allowed Morgan to go on a journey after this episode in season 5 to see how he catches up to Rick and the group," he said.
Fans can pick up "The Walking Dead" Season 6 on DVD/Blu-ray on August 23 -- only a couple months away from the seventh season premiere, Sunday, October 23 on AMC.