Am I the only asshole still watching this show? Anyway, I just watched the latest episode tonight and I have some theories on what might be going on.
In this episode, Skye is dying after having been shot a couple times by that asshole tech libertarian. They capture the dirtbag and are supposed to bring him back to SHIELD HQ but Coulson wants to do everything he can to save Skye, because that's the type of stand-up dude he is. He orders the plane to fly to whatever medical facility brought him back to life after Loki stabbed his heart in half. Fitz-Simmons are adorable again and solve the riddle of where to find the lab, and also name a mysterious drug that might help Skye. Bill Paxton and his agent Ward-type board their plane to try to turn it around, but Coulson convinces them otherwise because Coulson is so damn reasonable.
They find the facility, kill a couple guards that actually seemed too cool to be killed off right away like that, and find the HG drug. The place is rigged to blow so everyone bails, save Coulson, who needs to explore more because this is where he was raised from the dead. In it he finds this:
The upper torso of Dr. Manhattan, pumping his fluids into the HG drug mixture. Dr. Manhattan is DC, but in the Marvel universe, blue skinned humanoids are often Kree (a race of aliens that look human but also come in blue, as well as the regular Earth color pallet for people). This blue creature's fluids are pumped into Skye, and she immediately recovers rather than begging for death like Coulson.
The original Captain Marvel was a Kree soldier that came to Earth and died in an explosion, somehow infusing some of his powers with pilot Carol Danvers, the current Captain Marvel. Could Agents of SHIELD be setting up Skye to be the new Captain Marvel? I kind of hope so, even if it means changing the origin, I would dig Captain Marvel joining the greater Marvel universe.