At the end of the Iron Man 3,
Pepper Potts was infected with the Extremis Virus, which Tony then cured. As the scene is being narrated, he says something like, "Taking it one step further..." — before having doctors remove the shrapnel from his chest. This gives me the impression that the Extremis Virus is somehow related to him being able to remove the shrapnel from his chest.
Is this true?
It is not definitively resolved but we can make several suppositions:
If Stark had been able to remove the fragments before now, he would have done so rather than risk death aggravating his potential heart injury several times by driving his body to its limits.
He had been told it would be impossible to remove the fragments no matter how skilled the surgeons were, none were willing to risk it.
Since he was able to reverse-engineer the technology and effects of Extremis from Pepper, he would have both the technology to create the process as well as reverse it.
It would be logical for Stark to create a means of activating and utilizing the Extremis process in conjunction with an excellent surgical team because even if they made a mistake removing the shrapnel, a slight activation of the Extremis technology would repair any damage long enough for any surgeon to do their work. Why not utilize it to remove the shrapnel if he could?
An alternative answer could also be:
The giant electromagnet above the surgeon's heads may have been an invention created specifically by Stark to aid a previously unwilling surgeon to take the risk in removing the metallic shards.
In the comics, Tony infects himself with a fixed Extremis virus. This allowed Tony to connect to his network without a headset... he gave himself better reflexes and some of the iron man suit components in his body. The fact that they showed Tony talk to Jarvis without an earpiece tells me that he modified the Extremis virus and infected himself, which allowed him to heal from that kind of surgery.
Something that struck me as odd at the time was that, at the end of Iron Man 3, Tony says specifically that he has 'fixed' Pepper Potts Extremis infection, notice that he didn't say cure nor removed.
This leads me to wonder if he has indeed perfected the Extremis virus, thus leaning towards his own usage of the virus in Iron Man 4 or the next Avengers outing?
Tony narrates: The suits were a cocoon. I'm a changed man. I AM Iron Man. I expect Avengers 2 to show his extremis suits.
I think not, he was just carrying on with his
compromise to Pepper, exploding his armors and everything
My wife pointed out that he was able to do so because he gain knowledge of how to use
The extremis correctly, and some how he used extremis to heal.
Don't believe it was a virus nor was the vehicle for the drug a virus. I thought he used the reactor tech to develop a surgical procedure to make removing the sharpnel possible without the same level of risk.
Completing all the other answers, Tony says: "People say that progress is dangerous; They don't have to live with a bunch of shrapnel in their chests". IMO, this states that the "progress" was made towards the Extremis Virus. What isn't clear is how he used it: either only to remove the shrapnel or injected for an indefinite amount of time.
In Iron Man 3, Tony has the Ability to control all pieces and the suit itself with his mind. In the Comics, this is possible due to the Extremis Virus he's infected with. So, in the Movie, maybe the surgeon and the ability to control his suit with his mind are also just possible because he already has Extremis within him from the beginning of the movie.
