Spoilers for Agents of SHIELD's 100th episode ahead.
The Agents of S.H.I.E.L.D. 100th episode capitalizes on The Avengers and Ghost Rider story threads for the character of Phil Coulson (Clark Gregg). Gregg made his first appearance in the Marvel Cinematic Universe on the film side, being introduced as an agent of S.H.I.E.L.D. in Iron Man. He appeared in the movies until his untimely death in The Avengers, though his death acted as the unifier that brought the various heroes together for the film's final battle. Then, Marvel TV brought Coulson back to life for Agents of S.H.I.E.L.D., explaining his resurrection was the result of Kree technology used by Director Nick Fury under Project T.A.H.I.T.I.
While it's not clear exactly how the Kree resurrect humans from death, it seemed, at least in the case of Coulson, to be permanent. But we know from the revelations of future Yo-Yo that Coulson is dying. We theorized it could have something to do with the Kree substance called Odium, but the real cause of Coulson dying was revealed in Agents of S.H.I.E.L.D.'s 100th episode, "The Real Deal".
In the early half of the 100th episode of Agents of S.H.I.E.LD., the rest of the team discovers Coulson is dying when he loses his breath and passes out. After Simmons runs some tests, she reveals the mark on his chest is made up of "tissue that appears to have been dead for several years." Then it's revealed that Coulson's deal with Ghost Rider had to do with him sacrificing the rest of his revived life. He explains, Ghost Rider burnt through the "alien voodoo" holding him together. So what does that all mean for Coulson? It means he's dying, and there doesn't appear to be any way to save him. Further, he doesn't want the team to save him and we know based on future Yo-Yo's comments that if they do try to save him anyway, they'll bring about the end of the world.
Fans have wondered ever since Agents of S.H.I.E.L.D. premiered whether the show or the movies would deal with the fact that Coulson would ever make himself known to the superhero team he helped bring together. Marvel TV head Jeph Loeb finally revealed Coulson and the Avengers' reunion would be resolved in a "surprising way" - and now we know why. Certainly, revealing that Coulson is dying - again - from the wound inflicted by Loki is an undoubtedly clever way for the Agents of S.H.I.E.L.D. writers to bring Coulson's character arc full circle from his death in The Avengers. Also, if Coulson dies again from his same Avengers injuries, it renders a reunion between him and his superhero friends unnecessary.
The revelation about how Coulson is dying also capitalizes on the mystery about his Ghost Rider deal in season 4. That was a major unanswered question from the Ghost Rider arc last year, with fans wondering what deal Coulson could have made that allowed him to host the Spirit of Vengeance. Now we know it had to do with the fact that Coulson was resurrected and he sacrificed his second chance at life - and he's been slowly dying ever since season 4.
Going forward in season 5, it remains to be seen if the S.H.I.E.L.D. team will be able to find a way to save Coulson. He's been brought back to life once before, and as Daisy points out, they know the Kree are capable of resurrecting humans. But, with the fate of the Earth resting on Coulson dying - and Coulson having accepted his own fate - the Agents of S.H.I.E.L.D. writers have certainly set the stage for this long-running MCU character to die, and stay dead, by the end of this season. We know the Agents of S.H.I.E.L.D. season 5 finale is being written as a series finale, so it's possible that includes the final death of Phil Coulson. We'll just have to watch the rest of season 5 to find out what happens.
Agents of S.H.I.E.L.D. continues Friday March 16th with "Principia" at 9pm on ABC.