Whistler doesn't seem all that surprised to see Michael. We get a shot of him monkeying with the two cards (one of which is possibly an incomplete duplicate) and then he says, "You don't understand. Trust me." It's so cute how he thinks "trust me" will work. Whistler adds, "I'm not your enemy, Michael." Although Michael had ordered Whistler to summon Gretchen, she walks right in on her own, right past the gun-wielding Michael. Suddenly, Gretchen's capture whilst in a war zone makes a lot more sense.
Michael steps out of the shadows and points his gun at Gretchen, saying, "Despite everything, if Sara could weigh in right now, she'd tell me not to kill you. That's the kind of person she was. That's the kind of person you took from me." Gretchen turns to Whistler and says, "James? Didn't you tell him?" Whistler begins to protest, "He walked in--" "SHUT UP!" Michael orders. He demands that Gretchen look at him, aims the gun at her face, and says, "I never killed Sara." Michael replies, "I wouldn't expect someone like you to take this with dignity." Gretchen tries to muster a sincere look but her facial features are like, "What is this strange new behavior?" so she just looks kind of cross-eyed as she swears to God that Dr. Sara is alive. For that sort of invocation, I kind of hope that God strikes her down with a lightning bolt and booms, "So NOW you're calling on Me? When it's convenient?" Whistler looks frankly skeptical of both Gretchen's claims and Michael's ability to kill someone with anything less than a half-ton of dirt.
Gretchen spins a tale about how Dr. Sara managed to escape and "we knew if you found out, I wouldn't have any leverage. I fabricated the whole thing." Michael protests that Linc saw -- "A head in a box!" Gretchen says. You know if anyone from Prison Break ever makes it on to SNL, they're morally obligated to perform "Head in a Box" with Andy Samberg. (And why not? It's not like Samberg can do impressions. He might as well earn his NBC money for the week.) The back-and-forth comes to an end when Whistler whips out a pistol and aims it at Michael. He uses Michael's uncertainty about Dr. Sara to A) disarm him, and B) effect an escape before the cops show up. I hope for Michael's sake he gets back to his L.A. digs and shreds that "In the event of my death ..." letter. Since he's lost track of the stooges (who did manage to drop off the data card for the One World Conspiracy guy in the lobby), Michael will have plenty of time to do so.