From TVGuide, a recent interview with Matt Olmstead..
Key Points:
- Fan reaction did play into some of the decision to bring Sara back.
- Dr. Sara will be in for the entire Season 4.
- Prison Break 4 will start about a month (Prison Break time) after Season 3 ended.
- There are no hard feelings between TPTB and Sarah Wayne Callies.
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- So… I take it that wasn’t Sara’s head in that box….
Matt Olmstead: Yeah, that wasn’t.
But initially it was supposed to be her head. What changed?
Olmstead: What changed was … once we realized that the emotional hook of Season 3 was going to be the death of Sara, when we didn’t get the actress to do it, as soon as we wrote it and shot it, we realized that there was actually a way she could still be alive. Lincoln glanced at the head in the box for a split second. That could’ve been anyone. He wasn’t about to pull it up from the hair and inspect it closely. And then we were fairly careful thereafter of references we made to that and who took credit for it and what was seen or heard, and we left it fairly [vague]. But initially when we realized that we never actually saw the character get killed, we just had that knowledge in our back pocket and moved forward with the narrative as we intended. Which was: she’s out of the picture, Michael’s [feeling guilty] and Lincoln is freaking out because if they did that to her, they could do that to his son. It really gave us a real push for the season.
Don’t you think that was a little unfair to the audience — particularly fans of Dr. Sara — to jerk them around like this? They had every reason to believe she was dead.
Olmstead: I don’t think it was unfair, because it gave us some real juice storytelling-wise — it put teeth in the antagonists. Obviously they were now capable of killing somebody. It also gave us a couple of episodes where Lincoln withheld the information from Michael, and that gave us conflict with the brothers. But also, what were we really going to do? Were we going to see Sarah Wayne Callies tied to a chair for 13 episodes? And then if she broke free, what is she really doing? It was almost a disservice to that character to keep her around last season. Certainly, we could have put her on a cruise ship and she’s off sailing away. But we felt that if we’re going to lose that character, why not get the most drama out of it? We didn’t look at it in terms of [us] trying to tell the audience to go, you know, do something to themselves.
What role did the fan response to Dr. Sara’s death play in her return?
Olmstead: It factored in. It was kind of a confluence of events. We saw on the message boards that a lot of fans were wondering if she really was dead. And then that led to conversations of, “Well, what if she isn’t?” But then we put that on the back burner and moved forward with what we had to do, because it wasn’t anything that could be dealt with right then. And then when we came back after the strike and we realized that we were not going to finish Season 3… we creatively decided to blow it all out, jump forward in the timeline and get a fresh start. And so, when we pitched that, a lot of those elements remained, but we were still looking for that emotional core for Michael. We were kind of exactly where we were in the beginning of Season 3, which led to her demise, quote unquote. So we went back and revisited [the idea of bringing her back to life]. And once we started talking about it, it was mentioned again that fans are still wondering about her. And when people who are fans of the show — and of Sarah — are asking, “Is she really dead?”, what they’re saying, essentially, is, “I hope she’s not dead.” And then it became a kind of groundswell.
But then you have to get the actress to agree to return, which I assume was no easy task given the bad blood that seemed to exist last season.
Olmstead: There wasn’t bad blood on our side. It was a business decision. I understood where she was coming from in that she was given a provisional assurance that she was going to be a part of Season 3, but we had to revisit Season 3 a couple of times in the pitch stage in order to get it picked up. Fox was still looking for that emotional hook. Once we came up with the idea of her character going away, that gave us what we needed to push things over the edge. And although we were comfortable with it, she wasn’t. I also understand on a personal level how it factored in. She was pregnant at the time and looking forward to giving birth, and this wasn’t something she was interested in doing.
What changed for her that she’s willing to come back now?
Olmstead: She and I spoke a couple of days ago at length about what we have come up with creatively for her character…. We’re jumping ahead a little bit in the timeline. There’s a little bit of a mystery period for all of these characters in terms of how they got where they are and what happened to them. And we have some interesting things for her, and she responded to them creatively. We won’t just be picking up where we left off with her character. And she won’t be a damsel in distress waiting for her hero to return. There are some complicating factors involved with her character and things that she’s looking forward to. So we spoke about it, she thought about it, and we made a deal.
No hard feelings, then? Everyone’s moving on?
Olmstead: Moving on. She’s a very smart lady, and we’re all adults here. It was never personal. It was a business and creative decision, and we’re absolutely moving on.
Can you say how she’ll be reintroduced next season?
Olmstead: It’s going to be about figuring out what happened to her during that mystery period [between the end of Season 3 and the start of Season 4], and how she and Michael deal with it.
How much time will have lapsed?
Olmstead: About a month. Enough to jump past expected events that we left hanging at the end of Season 3, answering those things, but also moving forward.
And Sarah is onboard for the entire season?
Olmstead: Yes.
Source
After Michael decided to help out in taking down the company, he realized he is going to need all the help he can get, so he and Lincoln reunite with the rest of the gang, which is Mahone, Sucre, and Bellick. To protect his identity, Michael removed his tattoo. I understand why, but his tattoo is a symbol of what the show is about, and it was sad to see it go. 
Back at headquarters, Roland Glenn runs into a huge problem. Scylla is only a small slice of the “pizza” there are five other parts that they need to find. This is mainly what the rest of the season is probably going to be. Then at the very end, we see something is happening to Michael. He gets a bloody nose, which I’m guessing is not a very good thing. He might have some kind of brain tumor. 
