In the first episode it is indicated that Agents of S.H.I.E.L.D. happens after The Avengers, but the first episode also has Extremis in it. So is it a pre Iron Man 3 version of Extremis or post? I mean if it's post then why didn't they already have the Extremis solution (which is used on Pepper Potts)? So why to waste time in making Extremis again. Or is it a pre version?
Pulling from the The Comic Board Forum (and from IM3), we know that:
- December 31, 1999, Tony Stark learns about Extremis from Maya Hansen.
- October, 2006, Aldrich Killian injects himself with Extremis.
- February, 2008, Killian goes on to find new recruits (including Ellen Brandt, Chad Davis, Eric Savin, and Jack Taggert) to test Extremis on. Some of the recruits explode due to a malfunction, while others have limbs restored or other disfigurations fixed/cured.
- June 12, 2008, Chad Davis explodes from an Extremis malfunction which kills five others in the explosion.
- May 4, 2012, Battle of New York.
- December 19, 2012, Stark Industries security chief Happy Hogan is badly injured in an attack on the Chinese Theatre, which was triggered by an Extremis subject, Jack Taggart.
- December 24, 2012, Killian outs himself as the true Mandarin. He kidnaps Potts and subjects her to Extremis in an attempt to get Stark to help fix the problems with Extremis.
- December 27, 2012, With Stark's help, Potts' Extremis effects are stabilized.
- September 24, 2013, Agents Fitz and Simmons discover the explosion which occurs was from a person, as well as that it comes from the Extremis within the Centipede.
- September 25, 2013, The SHIELD team discovers that Michael is near exploding from a malfunction in the Extremis part of the Centipede.
These are the time based events. We do know Stark helped Potts make it through the Extremis transition. What I believe is not spelled out is we do not know if the "bad guys" know what that "cure" (or help) was which Stark provided to Potts. They (the bad guys) are still working with Extremis trying to fix these problems. The SHIELD team is trying to counteract the effects of the Centipede (people blowing up). They aren't necessarily trying to cure Extremis in these people.
EDIT: As seen in my revision of the chronology thread, I have made some updates to this thread here which makes more sense, but does not invalidate what I'm saying.