Ali continues to investigate the death of Khallid Fulani, but the Israeli embassy is not willing to give her any help, and all the paperwork on the case seems to have mysteriously disappeared. Ali finally locates Patricia Loftus, the woman who last signed out the file, but while she confirms Ali's suspicions, she tells her she signed an agreement never to disclose C.S.I.S.'s secrets. C.S.I.S. isn't the only thorn in Ali's side though; Pawlachuk and Mickey intervene to tell Ali to let it go, and advise her that they will not help her because they're not willing to put themselves on the line. When no one will back her up, Ali quits the force.
After Sonia's body is found on Columbia Street, Len is determined to find her killer, and recruits a group of kids to find Valentine du Bois. He's been staying in the jail, but Ali invites him to come stay with her on a platonic basis. The two nearly end up in bed while drinking one night, but Harper confesses his affair with Sonia to Ali, who feels terrible for him. He then confesses the truth to Wanda, who tells him that when he's ready, she'll be there. His sources manage to locate Valentine, and Len confronts him, arresting him and taking him into jail.
Nicco takes a lot of razzing from the other officers about going back on street duty, and soon finds himself involved in the case of a missing girl named Mimi. He also, at Billie's one-year anniversary at AA, begins a romantic relationship with Billie. Nicco finds Mimi and asks Billie to move in with him. When he and his partner try to intervene in a street argument, the man holds a knife on him. His partner fires, and Nicco falls. (It is not completely clear whether the bearded man stabbed him, or his partner accidentally shot him.)
While a montage plays, a crying Mickey comes into the office where Ali is packing up. Ali, Andy, Len, Mickey and Christine all end up down where Nicco was injured, and watch as his body is loaded into a body bag. Billie arrives in a taxi, and Len restrains her from going to the body. The show ends with Ali at the home of a man whose daughter had gone missing. She was going to tell him she quit the squad, but when he showed her his daughter's diary which he had just found, Ali decided to take on the case on an off-the-job basis.