In Absentia, Season 3, episode 1, opens with Emily dreaming that Julianne Gunnarsen, the special agent who killed Alice, shoots her point-blank in her chest. She also dreams about her house being explored, suggesting the trauma she has gone through and the truth about Alice's death she knows.
The show then escalates to Nick getting intel from his source about the brutal organ trafficking ring. The limited time compels him not to call his FBI team but to take Emily along to the ground, despite being suspended, involving her directly in the case.
Read on to know the complete recap of Absentia season 3, episode 1.
Complete recap of Absentia Season 3 Episode 1
By season 3 episode 1, Emily is seen living with Nick and Flynn. Absentia makes it clear that Nick and Emily aren't together but are only co-parenting Flynn. Flynn has joined swimming classes, and his coach, Mr. Rizzo, is the one Emily is concerned about. She finds some military photos on his social media. Emily breaks into his apartment and discovers a handgun when Mr. Rizzo returns.
Emily eventually escapes when Rizzo is talking to his mother on the phone, as she gets an opportunity. Meanwhile, Nick is investigating three murdered young men whose bodies were dumped with several body organs missing. This suggests involvement of some Black market organ trade and ritualistic crime.
What makes Absentia more interesting is that Nick's superior is none other than Julianne herself, who was cleared of wrongdoings in Alice's shooting. Nick has now stopped attending mandatory counselling and insists he wants to forget everything. He is determined to put his trauma and past behind him, but has clearly not processed it.
Emily then invites her brother Jack for a family dinner, and Jack breaks down seeing Alice's clothes. Emily realizes that Jack and Alice were having an affair, which makes Emily furious, and she warns Jack that Flynn must not find out about it.
Through his source, Nick is warned about something major that is about to happen tonight related to the organ case, and Nick is given an address. She also informs him that after that, she will need protection, and things are unfolding too fast for Nick to call the FBI team. Nick decides to take Emily with him, and this is what pulls her into the case directly.
How does Season 3, episode 1 of Absentia end?

Nick and Emily do what the source woman says. They follow her to a warehouse and uncover the organ-harvesting ring, which was horrifyingly huge. They find a row of empty mattresses and bodies wrapped in plastic. There was also an operating room where organs were removed, and Nick indulges in a fight with the guard while Emily chases the surgeon, who has a cooler filled with organs.
The surgeon becomes aware of the suspicion and tries to run in a van, but Emily clings to the driver's window and forces him to crash. This panics him and makes him run away on foot, leaving behind a bag full of organs. Julianne gets upset when she learns about Emily's involvement in the case despite being suspended. Julianne also claims that she has still caught Emily watching her house twice, which suggests that she still suspects her.
Nick is informed by his source that they have messed up and runs off. Nick, while being on the call with Emily, is ambushed by three men and is brutally beaten. Emily hears all of this on the call and takes Cal's help and rushes back home. The house is destroyed while Nick is no more there. Moreover, one sttacker is still there, and as she confrots him, the man stabs her, leaving the episode in a shocking cliffhanger.