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In the finale of Chuck Season 4, Morgan finds a corrupted version of the Intersect in the box belonging to Chuck and uploads it to his brain.

Who build those glasses? And who took it to the Castle?

I think, there are only three big bad guys in the story left at that point:

  1. Decker (who was blackmailed by Chuck a few moments ago)
  2. Shaw (sitting in jail) and
  3. Quinn (who is likely not to have the resources to do this).
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    It's been a while since I've watched the show but, I'm curious if you've continued watching the series after this episode. Sometimes they show explanations in later episodes... and sometimes you just have to accept things. – Catija Jan 29 '15 at 6:32
  • @Catija: Yes, I know that they explain things at some point, but I've watched it till the end, but I did not notice a direct explaination for it. – Markus Klein Jan 29 '15 at 6:34
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In Episode Six of Season Five Chuck Versus the Santa Suit - Daniel Shaw is revealed to the be the mastermind of the conspiracy to destroy Chuck.

From his prison cell while being interrogated by Clyde Decker, Daniel Shaw flashed on all of Deckers "dirty secrets" and started to black mail him as a pawn to destroy Chuck.

So to answer the question, Daniel Shaw probably instructed Decker to create a corrupted intersect glasses but Decker was the one to put them in the personal belongings that "General Diane Beckman" supposedly left behind for Chuck.

I believe there was more dialog alluding to this plan in this episode and its a great episode to rewatch anyway :-)

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