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Before Whistler was incarcerated in the Sona Federal Penitentiary, he allegedly was a fisherman, running a charter boat between America and Australia. One day, he got a call demanding to know exactly where he took a naturalist of some sort who took water samples and measurements. He then worked for Gretchen Morgan. He said he couldn't remember – but then government types started snooping around. When James had a bar fight, he killed the Mayor's son, leading to his incarceration in Sona. The people who are trying to get him out demand that as soon as they do, he show them where he took that guy. After he was transferred into Sona, he hid into a crawlspace as most inmates wanted to turn him in to The Mayor for their freedom.
Whistler was first found, because of Bellick behind a wall. Bellick later reported to Michael in exchange for water where Whistler was hiding himself, but Mahone found him first. Whistler said to Mahone that he was the typical policeman, having a wife and kid, couldn't sleep well and was a drunk. Whistler, Michael and Mahone then tried to escape, but they failed.
Whistler later escaped with McGrady, Michael and Mahone. Whistler was running away before the exchange and Lincoln did attack him. While finally changing from places with LJ, Whistler was running away with Gretchen and did leave his love, Sophia Lugo. Whistler was later seen with Mahone and Gretchen, leaving the bar.
After Season Three
Between the 3 weeks, Gretchen, Mahone and Whistler worked out a plan to get a Scylla-card and make an end to the Company.
Mahone takes Whistler to Stampede Industries to retrieve Scylla. Whistler then kills Jason Lief inside the hotel and takes what he believes to be Scylla. He was in the process of copying the card when Michael interrupts him, making the card copy incomplete. Later on, he gave the copy to Tuxhorn and kept the original for himself. Mahone tells Michael that he and Whistler have been working against The Company to destroy it. After The General realizes the card was a duplicate, he sends Wyatt to kill Whistler and retrieve the original card. Whistler then was shot by Wyatt from the back of head and his dead body was later found by an unknown person.
Donald mentioned to Michael that Whistler should give him the first Scylla-card, but never finished this because he was killed. He also later appeared on a picture in Going Under. Whistler was a few times mentioned by Michael, Mahone, Miriam Holtz, Gretchen and T-Bag. Following Whistler's death, T-Bag did take over the role from Whistler as Cole Pfeiffer.
When T-Bag was in troubles, a few men rescued him. T-Bag then saw a paper and explained that his friend, Gary Miller died. T-Bag then was using the key from Whistler and changed his name in Cole Pfeiffer and even thanked him. T-Bag then was changing the passport, so he could have access to GATE.
Whistler's name later appeared on Michael Scofield's list. It was a list made by Michael, which deaths the Company was responsible for.