While following up on a lead, Alec and the others attended a party thrown by the High Warlock of Brooklyn, Magnus Bane, who openly flirted with Alec.
Alec then accompanied Jace, Isabelle, Clary, and Simon to retrieve the Mortal Cup.
His parents were sent to run the New York Institute, where he would grow up.
Isabelle insisted on watching the exchange between the Inquisitor and Valentine, and was thus witness to Valentine turning down her offer to save Jace as well as the Inquisitor's surprised reaction to his decision.
Maryse demanded that the Inquisitor set Jace free and, realizing that she had imprisoned an innocent child, she was about to agree until Alec told them that he had already escaped and was on the way to Valentine.
Alec Lightwood is a Shadowhunter and is the older brother of Isabelle and Max, as well as the adoptive brother and parabatai of Jace Lightwood Herondale. Since queer Shadowhunters are normally shunned by the Clave, Alec was skeptical about coming out.
He eventually overcame his worries and revealed his relationship with warlock Magnus Bane to his family, friends, and fellow Shadowhunters—an act that inspired other closeted Shadowhunters to come out about their sexuality, as well.