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In the Agents of SHIELD episode The Magical Place, it is shown that

Coulson's brain is being operated by a giant robot. Though his heart is not being operated on, the region where he was impaled. Therefore the brain was being operated upon to alter his memory to "make him the man he once was."

But why wasn't his heart being operated upon?

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Presumably because they'd already fixed the heart.

He was alive, after all. His heart had been filleted, and the process to bring him back to life is what robbed him of the will to live.

The brain surgery came after they'd restored him to life and seen "the thing he'd become."

  1. Coulson dies.
  2. Coulson is brought back to life through unspecified means.
  3. Coulson's quality of life is awful because his memory of Step Two is too horrible to bear.
  4. Coulson gets brain surgery to replace his memory of Step Two and Step Three with a Magical Place.
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  • could ity be that that body was actually a clone?
    – Adeetya
    Jan 8, 2014 at 12:33
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    @Adeetya I think we haven't been given enough information to support or debunk any theory, really, so--sure, it could be a clone. We have no reason to think it is or that it isn't. (He does have those scars, though.)
    – BESW
    Jan 8, 2014 at 12:34
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    I think there's a strong implication that he's not a clone, since the doctor says they did at least seven surgeries on his long-dead body to bring him back. That seems overkill for a clone/LMD/etc, though anything's possible...
    – KutuluMike
    Jan 8, 2014 at 13:10
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After the scene you mention showing an operation, there is another scene.

In the second scene Agent Coulson talks to Dr. Streiten (played by Ron Glass) in the doctor's car.

Coulson questions the doctor regarding what happened and it is revealed that the operation on Coulson's brain was the 7th procedure required after Coulson had been dead for days (rather than the seconds originally stated).

It isn't stated unambiguously, but I interpreted the scene to mean that at least some of the first six procedures involved Coulson's heart.

Also, there was this dialog

Coulson Why was that machine messing with my brain?

Doctor After what you'd been through we wanted to restore the man you'd once been so we gave you a pleasant memory.

Which again, I interpret to mean that the operation on Coulson's brain was not actually necessary to restore his life.

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  • Coulson actually determined that the "revive from the dead" - Tahiti - that he designed, required re-writing the memories. He was the one who wrote that the memory had to be changed after determining how to "resurrect" an avenger.
    – EngrStudent
    Feb 5, 2015 at 2:10

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