Agents of S.H.I.E.L.D. has toyed with the idea of the multiverse before, but the series hasn't really explored its potential -- at least, not yet. Season 4, which released around the same time as Doctor Strange, introduced the idea of the multiverse with the debut of Robbie Reyes' Ghost Rider. Like the Sorcerer Supreme, Ghost Rider can tap into the multiverse's energy and open portals to other dimensions. Likewise, in Season 5, Coulson's team had to deal with the Fear Dimension after the Kree monoliths exploded in the Lighthouse, opening a rift in space-time. This caused one world to leak into the other, allowing manifestations of the team's worst fears to wreak havoc on their bunker.
Since the multiverse has long since been established, Season 6 could take a deep dive into the implications of alternate universes. This version of Coulson may be from a dimension where S.H.I.E.L.D. doesn't exist or stayed underground. He could come from a post-apocalyptic world or one with technology so advanced that it has easily mastered the art of inter-dimensional travel. The possibilities here are truly endless. This seems like one of the most likely explanations for Coulson's Season 6 doppelganger.
In the comics, Life Model Decoys are a S.H.I.E.L.D. favorite. Director Nick Fury, in particular, has an infamous LMD habit; if he senses danger, he'll send a LMD of himself instead of showing up in person. In fact, this particular trick has saved his life on several occasions -- and it could explain how Coulson returns on Agents of S.H.I.E.L.D.
LMDs debuted on Agents of S.H.I.E.L.D. in Season 4. Created by Dr. Holden Radcliffe, an LMD called Aida fostered the development of the Framework, a virtual world that erased the regrets of its users. This created a mess of a reality, where Hydra never fell, Inhumans were hunted down and our main characters were scattered across the world. Coulson's team ultimately destroyed the Framework, but at least one LMD survived until midway through Season 5: Anton Ivanov, aka the Superior (or was it MODOK?).
Though Ivanov ultimately met his end at Yo-Yo's hands, his survival could mean that other LMDs managed to survive the destruction somehow. What's more, he had plenty of time to build more LMDs like himself and stored them away in case of emergency. If this is the case, his archive would likely be incomplete, considering the destruction of the Framework and all its facilities. As such, a Coulson LMD could be reprogrammed with a completely different backstory. Indeed, it may not even know it is based on someone else. This would explain why Season 6's Coulson doppelganger doesn't know what S.H.I.E.L.D. is.
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