Okay, so Michael leaving Sona just means he leaves the building, and gets to stay in a box outside instead. That said, I can see how this is worse.
First, Michael gets dragged into the general's office and is asked about his escape attempts. Michael denies everything. When he won't talk, they stick him in a hot box. Just a tiny box, wrapped in plastic wrap that bakes in the sun. There is zero chance this is legal. He'll 100% die if they leave him in there for more than a few days. And they tell him this. So, I guess they don't care that it's illegal.
It doesn't take long for Michael to start talking. He tells pretty much the whole truth (at least, as much as we can see) about the Company and how he's supposed to break out Whistler. And he tells him that LJ has been taken hostage. The general thinks this is a batshit crazy story (and who can blame him), but he drags Whistler in to corroborate it. Which he does, but he's not happy about it. He also tells them Susan's real name.
The general heads out to pick up Susan and bring her back. He tortures her for a while and eventually she cops to being a part of it. But just a tiny part and claims all she did was babysit LJ and that's her only role. Lies. Anyway, she agrees to take them to where LJ is being held. However, when they get there, LJ is gone and she manages to kill the general and the other soldier with them. A new general shows back up and brings Michael and Whistler back inside the prison.
Back inside, Lechero is losing some of his status. Sammy is starting to make a name for himself and bypassing Lechero on decisions. Pocket Boy is not happy about this since Sammy hates him and he's got a pretty decent thing going with Lechero. So, he approaches Mahone (oh yeah, he's back inside too) and tells him he'll supply him with free drugs if he kills Sammy. But, Mahone wants to get clean, so he tells him no.
However, Sammy meets with the guy that had Sucre smuggling stuff into the prison. He tells him he needs to make a move on Lechero and the answer is in the package. When he finally opens the package, we see there is a gun inside it. I guess next episode we'll be going after him, but something will go awry.
Oh and Lincoln and Sucre come up with a plan to make the Company think they are fighting, and it works, but I honestly do not have any idea why they did this. Was it just to see if they were being watched all the time?