End of the Tunnel is the 13th episode in the series. In this episode, Michael found his plan has went wrong and has to rethink the escape.
Abruzzi is flown out of the prison to a hospital after his throat was cut with a razor blade by T-Bag. With Lincoln now in the SHU, the five remaining inmates discuss what is going to happen. Michael wants to postpone the breakout until he finds a way to get Burrows out of solitary confinement in the 32 hours until his execution. However, the other four conspirators want to go as soon as possible. It becomes clear to Michael that the escape is happening that night.
After praying for Burrows with the prison priest, Michael gives a crucifix necklace to the priest asking to send it to Burrows. The priest agrees and gives it to Burrows in confinement. Burrows finds that the crucifix has been tampered with, and after pulling it apart he discovers a hollow area in the back of the cross contains a small black pill, along with a tiny piece of paper that read "EAT 8:10". Michael had hidden it previously in order to get Lincoln into the infirmary. Lincoln takes the pill at 8:10 pm, 50 minutes before the breakout, and suddenly collapses onto the ground, grasping his stomach. The guards promptly deliver him to the infirmary and Dr. Tancredi tells him that she believes he had had food poisoning.
The five escapees use the series of pipes to crawl to the vent underneath the infirmary, where Michael's group needs to enter to proceed to the wire that they must all crawl across to escape. However, when they arrive at the maintenance room which was right beneath the infirmary, Michael realizes the pipe which he had corroded previously, had been replaced. The team stare at Michael and the pipe which now effectively prevents the team from escaping through the infirmary. After a struggle to break the pipe with the help of leverage and Lincoln, trying to push down onto the pipe from above, the group is unsuccessful. Dumbfounded and distressed, Michael says "We're not getting out of here." The episode ends with T-Bag pulling out a shank and threatening Michael, "Unfortunately pretty, that ain't an option."
- End of the Tunnel refers to the situation the team faced in the end of this episode - the tunnel which led them to the escape was blocked.
- "End of the Tunnel" was also the final episode to be aired in 2005 in the United States and Canada as it was the last episode in the first batch of thirteen episodes ordered by Fox. The series was extended to a full season of twenty-two episodes by Fox on September 29, 2005 due to its popularity. The hiatus allowed the production to catch up and the next episode was aired on March 20, 2006.
- This episode attracted an average of 12.1 million viewers in the United States on its original air date, making it the most watched episode in the series so far.
- A clip of this episode's final scene was used in the 63rd Golden Globe Awards during the announcement of Prison Break's nomination in the category of "Best Television Series - Drama".
- The song heard in the background when the team gets ready for the escape is "The Outsider (Apocalypse Mix)" by A Perfect Circle.
In the alternative end ends just like the episode does, only a few glimpes at the same time are seen.