The Season 4 premiere revealed that Sara had actually escaped from Gretchen's custody. The explanation for the previous season's evidence was that:
In the premiere of Season 4 ("Scylla"), it is revealed that Gretchen Morgan had faked Sara's death. The head in the box belonged to a different woman who had a similar physical profile (tattoos and piercings) to fool Lincoln. Gretchen kept Sara hidden to use her as leverage later. prison break is sara really dead
: Gretchen Morgan, a Company operative, claims to have killed Sara after a failed rescue attempt. She sends a box to Lincoln Burrows containing what appears to be Sara’s decapitated head. The Reason for the Absence The Season 4 premiere revealed that Sara had
The saga of Sara’s "death" remains one of the most controversial and talked-about moments in Prison Break Gretchen kept Sara hidden to use her as leverage later
Michael delivers the confession. The trade is set. Then... nothing.
"That’s your trade," Gretchen says. "Give us Scofield, or the next box will have your son LJ’s head."