Absentia centers on an FBI agent who, while hunting one of Boston's most notorious serial killers, disappears without a trace and is declared dead. Six years later, she is found in a cabin in the woods, barely alive and with no memory of the years she was missing. Returning home to learn her husband has remarried and her son is being raised by another woman, she soon finds herself implicated in a new series of murders.
After years of assuming FBI Agent Emily Byrne was a possible victim of serial killer Conrad Harlow, she is miraculously returned to her family. Emily, however, has to struggle with the mysteries of her captivity and the fact that everyone has moved on without her. Investigating Emily's disappearance,, her husband Nick Durand detects a connection between Emily and a sex trafficker Robert Semerov, who has negative feelings about Emily. When the FBI traces the sex trafficker, suspicion suddenly moves to Emily. Is she still the same person they knew?
Emily's alleged serial killer, Conrad Harlow, is being released from jail, and Emily has not come close to solving the mystery of her kidnapping and time in captivity. As Emily struggles to return to normal life, a witness turns up and reinforces the suspicions of Emily. Emily denies the suspicions and is sure the witness is lying and was forced into making a false statement, maybe by someone in the FBI. Will Emily and Nick be able to find out the truth before Emily is again torn from her family?
When the testifying witness against Emily is murdered, all signs suggest that the murder was committed by Emily. While Tommy Gibbs and the Boston Police Chief are accusing Emily, she and Nick look for an FBI agent who forced the witness to lie. For Emily, there is suspicion that this agent is the one responsible for her abduction.
The evidence against Emily is too much for the FBI and Boston Police Department to ignore, so they ask her to turn herself in. In the midst of chaos, old feelings come to the surface between Nick and Emily. Emily decides she would rather flee and try to solve the mystery that is ruining her life. Can Emily save her relationship with Flynn? Is it possible for agent Adam Radford to solve this mystery? Can Nick trust Emily anymore?
When Detective Gibbs and Nick find an FBI agent who appears to have been murdered by Emily, the hunt for her goes up to a new level. With the help of a clue given to her by Adam Radford, Emily tries to tie all the threads while evading arrest. Nick tries to reconcile with Alice's betrayal. Can Emily save herself? Can Nick keep his family together?
Emily avoids arrest and finds another trace of the investigation. But with the disturbing new evidence, Emily begins to suspect one of her loved ones. Unfortunately, he is the only person who can help Emily figure out the case. Could it be just a little paranoia from Emily, or does she not have anyone to turn to?
Jack helps save Emily's life and finds a startling connection with Emily's childhood. Emily discovers secrets from the past that relate to a childhood friend, Charles. Meanwhile, Tommy arrests Jack for helping Emily. Alice confronts Nick, which puts both her and Flynn in danger.
Alice and Flynn are abducted by a mysterious person. Nick suspects that Emily was the one who kidnapped his family and desperately tries to find them. A reporter assaults Jack every time she wants to get exclusive information. Emily tries to get answers from Charles, but has to flee when Nick tries to arrest her. How will the couple act when they meet again?
Emily is able to retrieve more information from Charles and hopes that this will be a breakthrough in her research. Will this lead to Flynn? Will she discover the identity of who is after her? Will Tommy and Nick catch Emily and end the case that consumed the former agent's life?