KGB Habs wrote:There might be some spoiler if you have not read or played the breakout act.
In the Breakout conclusion, there is a possibility to interrogate Yelena. It is said in page BR33 that she hasn't been given full knowledge of the operation.
What's the cover up conspiracy within SHIELD? There is not a lot of detail. Are we suppose to know from the breakout act? Is it something left like that so the Watcher can create another act?
In the actual comics, the conspiracy isn't brought up again until Secret Invasion, which takes place a few years (real time) after Breakout. And the secret behind it all is revealed through no real effort on the part of the Avengers, really. So it could be anything you like.
I think at the end of Breakout in the comics, we see some shadowy off-panel figure offering Yelena revenge. That turns out to be (spoiler) Hydra - they turn her into a Super Adaptoid and she goes after the Avengers.(/spoiler)
EDIT: spoiler tag is apparently broken!