Clary returns to the institute, hurt and bruised. She demands to see Isabelle but Jocelyn wants to know where she has been and what happened. Aldertree interrupts them also wanting to know the same thing and asks to see Clary in his office.
Simon is woken up by his phone going off. Upon answering it he realizes that it’s his mother who is worried sick about him and wants to know where he is.
Back at the beach, Luke and Alaric are they investigating what happened. After speaking to a witness Alaric shows a sketch of Jace to Luke. Luke advises keeping this out of the mundane world as the pack should deal with it.
At the institute, Jocelyn goes to see Isabelle thinking she is with Alec but when she knocks on Alec's door, it Magnus who opens it. Annoyed and frustrated Magnus tells Jocelyn his honest opinion as to why he doesn’t get involved with Shadowhunter business. She convinces him to look at where he is now and she has done enough for Alec.
Clary is sat in Aldertree’s office. He asks her about what happened and if she knows about the ship in the river. Clary holds back and only tells Aldertree that she remembers Dot taking her from the street and then being in the river. Clary lets Aldertree believe that maybe Dot whipped her memory. After talking to Aldertree, Clary finds Isabelle and tells Isabelle everything. Isabelle is shocked that Clary lied to Aldertree and didn’t tell him everything. Isabelle and Clary are worried that they won’t be able to find Jace in time to save Alec.
Jace enters the Half Moon bar where all Shadow-world people and creatures go. Mia, a member of Luke’s pack, is behind the bar. Jace asks if he can make a phone call and, out of generosity, Mia gives Jace the phone and a pint on the house because he looks terrible.
Clary and Isabelle are trying to think of a way to try and find Jace, however, Isabelle's phone rings and it's Jace. Jace immediately asks if Clary's okay so Isabelle hands the phone over to Clary. Clary explains the situation with Alec to Jace and that Alec needs him right now. Isabelle has an idea and tells Jace to meet them at Magnus' apartment and they figure out a way to get Alec there.
After Jace puts the phone down he goes to leave but is stopped by Mia. She asks for his help because he's a Shadowhunter. She explains that one of the pack member’s god-daughter was kidnapped by the circle member and they need help to find her. What Mia doesn’t know is that Jace is actually the one who kidnapped her for Valentine. This is until Jace is recognized by a pack member, causing them to fight. Jace is thrown through the bar window and runs off bleeding.
Simon rings his mother and leaves a message telling her that he's sorry that he hasn’t called but his band has been on tour. He continues to lie to her but he does say that he will pop round the house to see her. Simon is interrupted by Raphael who frightens Simon and threatens him that he has to find Camille first because she is a threat to his family and clan. Simon, however, goes home to speak to his mum, ignoring Raphael’s threat, but she is not there. Simon goes to her room and finds a bottle of alcohol and the television still on. Simon, worried, rings Clary. However, she is discussing a way to get Alec out of the institute and to Magnus' apartment. Clary answers Simon’s phone call telling her the situation. Isabelle tells Clary to help Simon, she and Magnus have everything under control.
Luke is at the Half Moon bar showing Mia the sketch and she confirms that it was Jace. However, Luke reminds them of the rules, but they remind Luke it is blood for blood with the pack. Luke knows this and tells them that if it is true he will kill Jace himself, but Luke wants to know the truth.
Magnus and Isabelle are still with Alec in his room getting ready to leave. Aldertree storms in asking why Isabelle put in a request to transfer Alec to Idris. Isabelle reminds Aldertree it was her parents who put in the request. Aldertree declines the request and tells them that Alec will not be leaving the institute and will remain there. Aldertree puts a guard at the door to watch them. Magnus goes back to helping Alec. Alec mumbles something and a flashback begins. A teenage Alec and Jace are being tested. Jace reminds Alec that he leads the demons out of the dark and Alec reminds Jace that he does all the work. The simulation ends and Jace is over the moon that they passed the last test and he wants to tell Isabelle all about it. The flashback ends, and we return to today's time.
Jace is now running through alleyways trying to escape from Mia, who is taunting and following him. Jace collapses in front of a mundane. The mundane asks if he's okay and then sees the blood. The mundane tells Jace to stay still and rings 911. Mia disappears back into the alleyway.
Clary and Simon are scouring the streets for Simon’s mother. Clary, being new to tracking, is having difficulty tracking Simon’s mum. Clary and Simon talk of old memories about his mother which help Clary feel Simon’s mum and she can now track her.
Magnus, in frustration, throws the guard across the room using his magic as Isabelle bursts in to remind him that this will not help their goal of getting Alec out of the institute.
Jace wakes up in the hospital overhearing doctors. Luke and Mia show up at the hospital looking for Jace. Luke shows the sketch to one of the doctors and the doctor confirms that Jace is there, however, the doctor tells Luke that they still need to run tests. Luke and Mia head to Jace's room, but when they get there Jace is nowhere to be found. Splitting up to find Jace, Mia walks straight past him not noticing. Jace moves from his cover and heads out until he is stopped by the doctor. Due to this Mia notices and starts to turn, in anger. The doctor, not knowing what stands behind him, turns around and screams. Jace tries to reason with Mia but she launches forward and Jace runs.
Running up the stairs, Jace finds himself at a dead end with the door locked, however, Jocelyn opens the door and grabs Jace saving him from Mia. Jocelyn wants to help but Jace doesn’t want her help. Leaping off the roof and onto the ground below him, Jace runs off.
Isabelle is with Alec now, in his room. Aldertree enters and is quite concerned about how confident Isabelle is in her ability to save her brother. However, the body in the bed is not Alec, it is the guard shapeshifted into Alec. Aldertree, furious with Isabelle, makes a deal with her that she can save her brother if the consequences include Jace being arrested.
Magnus is back in his apartment with Alec. He is begging Alec to come back to come back to him. Magnus believes he has tried everything but takes a chance and kisses Alec, however, it does nothing.
There is a flashback of a young Isabelle training with her whip until she is disturbed by Alec who has doubts about becoming parabatai with Jace. Isabelle reminds Alec that they always make up after a fight and the only time anyone stops the parabatai ceremony is if one falls in love with the other. Alec looks at Isabelle and insinuates this is what he means. Isabelle tells him that one day he'll find someone who loves him, heart and soul, ending the flashback.
Clary and Simon find Simon's mum in a café. Simon is relieved that they have found her and he tells Clary this as, because of her, he might tell his mum the truth concerning who he is. Clary's phone rings, it’s Isabelle. Isabelle stressed, updates Clary about Luke's pack wanting Jace dead because they believe it was Jace, but Clary clarifies that it wasn’t Jace but actually Valentine. Isabelle also tells Clary that she has made a deal with Aldertree, but believes that she won't get to Jace in time. Clary believes she might be able to get to Jace before the pack does.
Simon enters the café to see his mum. She is surprised and happy to see him. She tells Simon that she knows what's happened and explains that if it wasn’t for his band manager she wouldn’t know what has been happening. Simon is confused but interrupted by Raphael. Simon’s mum insinuates that this is his band manager. Simon is unhappy that Raphael is now threatening his family. Raphael, however, excuses himself as Simon is there but Simon's mum invites Raphael to join them for dinner. Simon doesn’t want this but Raphael accepts the offer before leaving. Simon and his mum are back at their home now and Simon, unhappy, explains to his mum that Raphael is not a nice person. Simon also informs his mum that he possibly might be returning home.
Clary, now at the Jade Wolf, tells Luke to tell the pack to back off because it wasn’t Jace who killed the wolf it was actually Valentine. Alaric interrupts them by telling Luke that Mia is close. They are near the Brooklyn Bridge and it looks like she moving in for the kill.
Jace is so close to Magnus' apartment but his path is blocked by Mia and some of the wolves. Jace explains that they can kill him but he needs to get to Alec first. After he is done with Alec they can kill him. Mia doesn’t know whether to believe him or not. Everything changes as Luke and Clary show up. Clary tells Mia that it wasn’t Jace, it was Valentine. Luke tells them to stand down but one of the wolves launches at Jace. Before he can do any damage Isabelle comes through a portal and hits the wolf with her whip. Isabelle declares that, by order of the clave, Jace is coming with her. Luke uses his alpha position to order them to stand down. Jace thanks Isabelle, but Isabelle doesn’t want his 'thank you' for what she has done.
Now at Magnus' apartment, Isabelle and Magnus are at Alec’s side as Clary paces the length of the room. Jace walks through, sets eyes on Alec, and rushes to him. A flashback begins of young Jace and Isabelle stood waiting for Alec to show up to start the parabatai ceremony. Cutting back to Jace, who is given the amust stone from Magnus, sitting at Alec's side. The episode goes back and forth from flashback to present day with Jace reciting the vows they took at the parabatai ceremony. Alec starts to slip away but Jace keeps going. Holding Alec, Jace recites one of the last lines of the vows and begs Alec not to leave him. Alec wakes slowly quoting the last line of their parabatai vows. Jace, and everyone else is happy to hear Alec's voice and are relieved he is back.
Aldertree interrupts and sentences Jace to the City of Bones to await trial for high treason for aiding and abetting Valentine. Alec is confused until Jace tells Alec that it will be alright and all that matters is him being back. Aldertree and guards escort Jace out of Mangus' apartment, ending episode three.