Sarah Wayne Callies, the actress who plays Sara, was pregnant during the filming of Season 3. Production schedules were tight, and she wanted to take time off for the birth of her child. The producers, however, wanted her available for filming a specific number of episodes.
Whistler left.
Yes, in Prison Break Season 3, it is made to seem that Dr. Sara Tancredi dies. Her severed head is shown in a box to Michael Scofield as proof of her murder by Gretchen Morgan (Susan B. Anthony). However, this was due to behind-the-scenes contract issues with actress Sarah Wayne Callies. The show later retconned her death in Season 4, revealing that Sara was alive and the head in the box belonged to someone else (Gretchen’s assistant). does sara die in prison break season 3
Here is where the "Does she die?" question gets tricky.
Gretchen Morgan admitted she never actually killed Sara. She sent a fake head—belonging to another woman who had helped Sara escape—to maintain leverage over the brothers. Sarah Wayne Callies, the actress who plays Sara,
When the show was renewed for Season 4, the writers needed to course-correct. Fans were outraged by the character’s gruesome treatment, and the chemistry between Wentworth Miller (Michael) and Sarah Wayne Callies was too valuable to lose.
The box was small, wrapped in brown packing tape, and it arrived with a note that had no name—only an address: Sona, Cell 40 . Michael Scofield didn’t need to read it. He already knew. Whistler left
In the third season, Sara is kidnapped by The Company along with Lincoln Burrows' son, LJ. In the episode Lincoln is led to a box that appears to contain Sara’s severed head. For the remainder of Season 3, the characters—and the audience—are led to believe that Sara has been brutally murdered by the Company operative Gretchen Morgan. The Twist: Is Sara Actually Dead?
Early in Season 3, it is revealed that Sara and LJ Burrows have been kidnapped by "The Company" to leverage Michael Scofield into breaking James Whistler out of Sona prison.