Captain Marvel is just around the corner and, with it, the Marvel Cinematic Universe's version of the Skrulls. The Skrulls, of course, are a race of shapeshifting aliens with a nasty habit of trying to invade Earth. Notably, Coulson will be heavily involved with the events of Captain Marvel, which takes place in the mid-90s. As such, he has some experience with Skrulls -- and the Skrulls will have some experience with him.
It will be hard to tell how Agents of S.H.I.E.L.D. will deal with the Skrulls until Captain Marvel releases in theaters next month. However, it's possible that a subtle Skrull invasion set in present day could lay the groundwork for Season 6's Coulson doppelganger. Perhaps this Skrull glimpsed Coulson during Captain Marvel and mimics his appearance when he returns to Earth on Agents of S.H.I.E.L.D. On the other hand, a Skrull could assume Coulson's appearance based off a picture, or a hologram like the one Mack uses in the Season 6 trailer. Either way, the Skrulls would provide an easy explanation for this mysterious doppelganger.
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Or Agents of S.H.I.E.L.D. could try something completely new. The show has borrowed quite a few comic book conventions over the years, but there's a major one it hasn't tackled yet: clones. As controversial as they may be, clones are a staple of comic book mythology, from Spider-Man's infamous Clone Saga to the X-Men's Madelyne Pryor and Wolverine clone X-23. By exploring clones, the series would wade into uncharted waters, but -- like the seasons that have come before it -- that could be exactly what the show needs. A fresh, MCU-inspired take on clones could also provide a succinct, compact story for the show's shortened sixth season.
Lastly, it's possible all of this is a misdirection of some kind. The show's stars could be trying to throw fans off in order to keep the mystery going. If that's the case, this could be a simple resurrection -- something Coulson is no stranger to. He was implanted with false memories the last time he was resurrected; if that process went wrong, he may forget everything, not just the process itself.
That being said, this is the least likely scenario. The show gave Coulson a poignant, emotional sendoff in Season 5. By resurrecting him (again), his return would cheapen this major moment in the MCU canon. As such, this is unlikely, but worth considering all the same.
Agents of S.H.I.E.L.D. is set to return for its sixth season in July 2019 on ABC with 13 new episodes; the series stars Ming-Na Wen, Chloe Bennet, Henry Simmons, Iain De Caestecker, Natalia Cordova-Buckley and Elizabeth Henstridge.