On the season finale of Alcatraz…
Tommy Madsen is given a blood transfusion containing colloidal silver by a scientist working with the Warden.
For surviving, Tommy is given one request by the Warden. At first, Tommy wants to see his son, but after the son runs from him, Tommy changes his mind. He makes Ray Archer the adoptive parent and simultaneously has him fired from his position as a guard from the prison. He also tells Ray that he did commit the murder.
Within the secret room, the scientist and the Warden discuss all of the exact location and times of the inmates reappearing. They can also track them.
Tommy is given the role of the advance man in exchange for his freedom.
Rebecca learns from her boss that her former partner was under investigation for receiving money from Harlan Stillman's company.
Tommy hunts down Joe Limerick for the final key, but Joe kills himself. Diego is able to find the key on his dead body.
Emerson makes a deal with a higher up official to try and get Lucy to safety but she refuses to leave him.
Rebecca chases after Tommy, capturing him briefly before he stabs her.
Emerson and Lucy finally unlock the secret room to discover instruments and a map that gives the locations for where all the inmates will be, including outside of San Francisco.
They also discover the scientist.
Rebecca flatlines from her stab wound.