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:
- Decker (who was blackmailed by Chuck a few moments ago)
- Shaw (sitting in jail) and
- Quinn (who is likely not to have the resources to do this).