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The Message was a taped recording of Michael and Lincoln that was created to, apparently, clear their names by giving out all the information they had on The Company.
The message opens with a close up on Lincoln saying "My name is Lincoln Burrows. And I'm innocent." He then continues to say that he was set up by a group named The Company and that the real Terrence Steadman committed suicide the night before in the Cutback Motel in Montana. The camera then pulls back to reveal Michael next to him, and Michael continues to comment on Steadman and then goes on to comment about The Company, Alex Mahone, and Oscar Shales. The message goes on until Michael begins to talk about Sara, saying how he was sorry and using many "phrases" she might have understood.
The message at first was to be an honest statement that would have the full intention of stating what was really going on, and to send a message to Sara. Kellerman being with them, said it was the wrong play. He said that if they said the message the way they planned, it would play "too earnest". Lincoln agreed, saying that was the point, to tell the truth. Kellerman then continued to say that "the truth sends them home to their wife and kids, lies will keep them busy". Lincoln objected, stating that it was their one chance to say it how it was, but before he could barely finish the statement, Kellerman became inpatient. He told Lincoln that he could do what he wanted but he knew how the tape would be broken down. Michael told him the message was different compared to a terrorist-sent video, but Kellerman said to the government, it was the same. Michael then suggested a distraction that would keep them guessing to buy them more time. Kellerman liked the idea, and they went along with the tape as planned, with Kellerman's edits to the plan.
Kellerman: If you say it that way it plays too earnest.
Lincoln: Of course it will, it's the truth.
Kellerman: Okay, but the truth sends them home to their wife and kids, lies will keep them busy.
Lincoln: I'm not tellin' a lie to the whole country. It's our one chance to say it how--
Kellerman: --Say whatever the hell you want. Tell them you're the green lantern, but I know how they brake down these tapes. I've done it. Every detail matters. Bin Laden crosses his legs right over left, tells us something completely different than left over right.
Michael: It's not the same message.
Kellerman: To them, it is. If you want this plan to work, whatever you're saying with your mouths, you need to be saying something different with your bodies and your eyes.
Michael: Slightly up and to the left?
[Referring to Michael's Distraction; The water is warm]
Michael: We've been throwing them a bunch of fastballs. What do you say we mix it up a little?
Kellerman: Like what?
(FBI analyzes the morse code to reveal the water is warm as Michael's distraction)
Lincoln: What the hell does that mean?
Michael: Nothing. It'll take the feds a while to figure that out.
The real purpose of this message was to get the attention of Sara. They needed to meet up with her because she had a key to a deposit box at the Corona de Oro club in Chicago containing the tape. Michael was using special phrases to get her attention such as "Second Chance", "Every Doctor's Nightmare", and "Safe Haven". These were actually name's of chapters in the Big Book of Alcoholics Anonymous. Sara, knowing the book, realized after multiple viewings what Michael's message was.