The moment is brutal. Michael vomits, and audiences were left in shock. The show’s primary love interest, the moral compass of the series, was apparently murdered off-screen by Gretchen Morgan (Susan B. Anthony) on the orders of the Company. The on-screen decapitation was not an artistic choice; it was a business necessity.
The episode opens with Michael imprisoned in the hellish Sona prison in Panama. Lincoln hands him a box, claiming it was found on the boat where Sara was last seen. When Michael opens it, he finds the grisly contents: the severed head of Dr. Sara Tancredi.
Actress (Sara) did not leave the show voluntarily. According to multiple reports from 2007, Callies was fired due to a breach of contract. During the Season 2-3 hiatus, Callies was pregnant. She requested time off or reduced hours to care for her newborn. The producers, operating on a tight filming schedule, felt this conflicted with their needs for Season 3.
But how do you bring back a character whose severed head was in a box? The answer was a classic Prison Break hand-wave.
Here is the definitive breakdown of what happened to Sara Tancredi, both on-screen and behind the scenes. At the end of Season 2, Sara was on the run with Michael Scofield and Lincoln Burrows. When Michael surrendered to the FBI to buy Sara and Lincoln time to escape on a boat, it seemed like a temporary goodbye.
So, if you are binge-watching Prison Break today, do not despair at Season 3’s cliffhanger. She just took a very messy, complicated detour through television hell—and survived to tell the tale.
Negotiations broke down. In a 2015 interview with The Hollywood Reporter , Callies stated: "I was fired for wanting to be with my family. I didn't quit… I was told I was no longer needed."