When Alicia listens to wire-taps made by the FBI she realizes that Will has left her a second voice message.She goes to his office to ask him about it, but Tammy is there.He confronts Baxter and tells him he is going to jail.
When Alicia confronts Will about the second message, he lies to her and says that he thinks she made the right choice staying with Peter.
After Alicia's discovers that Peter had sex with Kalinda, she separates from him.
Throughout the series, Will shows an attraction to Alicia Florrick.
In the episode "Heart", Will and Alicia share a passionate kiss in his office as Alicia is comforting Will after a case. Realizing she has made a mistake, she does return, only to have missed Will because he had stepped out.
After winning a case, Will and Alicia go out to celebrate.