Fire/Water is the 46th episode in the series and the second in season 3. Michael must rescue the mysterious James Whistler before Mahone kills him. The inmates are brewing a riot because of the lack of water supply.
In Sona, Michael begins his search for Whistler by talking to Bellick about the note slipped into his pocket during the fight yesterday. Michael goes into the sewers and makes contact with Whistler, supposedly a fisherman who was jailed for killing the Mayor of Panama City's son in a bar fight and is hiding from the other prisoners because of a bounty on his head. At the same time, a scuffle between one of Lechero's cronies, Sammy and another prisoner results in the spill of Sona's entire water supply.
Lincoln meets with "Susan B", the woman from the bar, and is tasked with reporting in every day on the progress of the escape. According to Susan, due to the political spotlight on Whistler, the Company cannot simply bribe someone or raid the prison to free him, resulting in their recruiting of the brothers. Later, Lincoln visits Michael and gets Whistler's note.
In Panama City, Fernando Sucre buys a gun and ammunition and goes to Sona to see Bellick, threatening to shoot the ex-CO unless he reveals Maricruz's location. Bellick confesses that he never kidnapped Maricruz, but instead simply drove her off the property and faked the kidnapping. Sucre leaves to return to Chicago and runs into Lincoln, who advises him to walk away from his family in order to "keep them innocent". At a bus station, a run in with police convinces Sucre to call Maricruz in Chicago and tell her that he won't be returning, since his involvement in her life has only lead to trouble. They exchange tearful goodbyes and love messages before Sucre hangs up and walks away, leaving the crucifix necklace on the phone.
Bellick, as an "untouchable", is unable to get food, water or clothing. When Michael evades his pleas for help Bellick begins to question why Michael was interested in the man in the sewers. Mahone is also curious about what Michael is up to, and learns from another inmate about Whistler and the bounty: in a deal worked out between Lechero and the late Mayor's family, any inmate who kills Whistler will be granted a court date with a friendly judge, effectively giving them a pardon for their crime.
After seeing Michael return from a trip down into the sewers, Mahone journeys down there and finds Whistler. At the same time, Bellick gets T-Bag to set up a meeting with Lechero and is able to negotiate some food and clothing in exchange for his information on Whistler. Lechero's thugs go to the sewers to capture Whistler, but Mahone has already dug him out of his hiding place and, armed with an iron pipe, slowly makes his way back to the surface. Michael sees Bellick with clothes and food and realises what has happened. At the same time, an outspoken prisoner is using the lack of water to stir up dissension against Luchero's rule of the prison.
Lincoln manages to figure out that Whistler's note is referencing a bank in Panama. At the bank he sees Sofia Lugo, Whistler's girlfriend, as she withdraws something from her boyfriend's safety deposit box. Once outside, Lincoln confronts Sofia and takes the withdrawn object from her - a guidebook on birds - and gives her a message to deliver to Whistler. The Company observes the meeting, and the next time Lincoln meets with Susan B she demands the book from him. Once she leaves, it is revealed that Lincoln gave her a fake copy.
With his options short, Michael tries to make a deal with Lechero in order to get Whistler's bounty lifted, but Lechero doesn't even hear him out after T-Bag calls Michael a "back-stabbing snake". He takes matters into his own hands. He asked Tracy McGrady to obtain alcohol and plastic bags to create a crude explosive which he takes into an engineering section of the prison and places in a pipe. The situation is reaching breaking point, with the thirsty prisoners on the verge of total rebellion against Lechero and Mahone ready to collect the bounty on Whistler, when Michael's explosive detonates and clears out the blockages in Sona's plumbing, allowing water flow through the pipes and giving the prisoners as much water as they need.
In return for Michael's assistance, Luchero allows Whistler to rejoin the prison population, thereby denying Mahone his day in court. Later, Luchero has the outspoken prisoner drowned in a bucket by his cronies. The episode ends with Whistler thanking Michael for his help, and asking about how they are to escape; in response, Michael says that he has no idea.
How did Sucre bought the Gun past the guards in Sona???