This is the point where Michael is either near tears or indulging in a manful sniffle or two. Who can blame him? He probably thought there might be some making out, and instead, he's in the middle of what feels like talking to the angry ex, only they never went out in the first place. Michael finally pulls it together and tells Dr. Sara, "I am sorry about your father. I'm sorry for a lot of things -- for what I did to you. I have many, many regrets. But that's the biggest." Dr. Sara proves once and for all that she did make it through Don't Do Time in the Prison of Love AND its follow-up Don't Give Him Parole in Your Bed, and she tells Michael that his apologies really aren't what she'd consider "helpful" right now. So Michael apologizes some more. He puts the sunglasses back on like they were protective armor, then adds, "I didn't expect, uh, I didn't expect you to forgive me. But I don't want you to, ah... I don't want you to be alone in this." After the bad craziness dies down, Dr. Sara needs to revise her Michael Scofield stance, because having a boyfriend who can be properly penitent can be a good thing.
Aaaaand it looks like that stance revision is starting... now. Dr. Sara walks toward Michael, admitting, "I don't want to be alone," and they are thisclose to hugging but then Mahone has to ruin it all by heading down the road toward them. Michael orders Dr. Sara to get in the car, and she does, without going back and grabbing her purse first. Dr. Sara's handbag habits will be the death of me.
Once America's favorite fugitive un-couple gets in the car, it becomes clear that the only way Michael's going to get out of there is if he plays a game of chicken with Mahone and wins. Fortunately for all of us, he does. And then there are some more automotive hijinks and long story short, there's a car chase that ends up at an old factory. The real reason it ends up there is because you can't have a tense cat-and-mouse chase scene between Michael and Mahone in someplace that isn't simply teeming with hazardous substances and lethal objects, but the producers cover for that by having Michael crash his car into one of the factory's sheds.