Benson discovers one of the women in her rape counseling group is carrying an illegal gun and is forced to confiscate. Her actions lead to her counselor, Margo, reminding Benson that she's in the group to deal with her own anxiety over her sexual assault while she was undercover in a women's prison months earlier.
Margo also tells Benson that she needs her help in locating one of her patients, Jessie Crewes. Jessie was in the military, was raped by a fellow serviceman and is now seven months pregnant with his child. After Benson searches Jessie's abandoned car, she makes the gruesome discovery of her bloodied body in the trunk. Jessie's fetus has been removed from the body. Warner alerts Benson that the baby's life is danger because of it not being fully developed when cut from Jessie's womb.
The military refuse Benson any access to Jessie's files about her rape. They also inform Benson that Jessie was raped while in Iraq, meaning her crime scene is all but gone. The detectives also learn that Jessie has been listed as AWOL because she left her base camp in North Carolina in order to receive rape counseling in New York. Fin and Benson head back to Marlo's office, hoping she can help reveal more clues on Jessie's rapist.
Margo's hands are tied and she can't reveal any details from her conversations with Jessie. Benson and Fin find Michelle, another woman from the therapy group, who was good friends with Jessie. She opens up to Fin when she finds out he has a history in the military, too. She tells them that she didn't know Jessie's rapist, but she did know he had a higher ranking than her and that she was afraid because he was on his way back from Iraq.
ADA Greylek is able to dig up some loopholes in order to get access to the list of military personnel who were on duty the night of Jessie's rape. As the detectives are looking for possible suspects, Jessie's mom shows up and sees the pictures of her daughter's dead body. Benson quickly ushers her into the interrogation room to talk. Her mom tells her that Jessie never named names and said she faced harassment from other soldiers after the attack.
After finding out that Jessie received a lot of harassment from a fellow soldier in her command post, Fin and Benson go to his New York hotel looking for him. Inside, they find Dominic engaged in a fistfight with another man. As Benson tries to break the men up, she gets slammed against the wall. She instantly freezes up and goes into shock. Fin breaks up the fight and puts Dominic in handcuffs, but remains concerned about Benson's reaction. Especially since after she snapped out it, she held her gun to Dominic's head.
Benson interrogates Dominic about his relationship with Jessie. He insists they are just friends and he was concerned about her, which is what led him to New York. He swears that had hadn't seen her in over five months. Benson's hands begin to shake and Dominic takes notice. Meanwhile, the other man involved in the altercation is a fellow soldier, Gary Rostum. Fin takes him to the other interrogation room.
Fin starts probing for answers from Gary. He says that he and Dominc came to blows over Jessie and her affair with Gary. Meanwhile, Dominic doesn't flinch when Benson reveals the crime scene photos. She leaves and later returns with a signed statement stating that Jessie's landlord saw her arguing with Pruett just before her murder. Pruett reluctantly allows Benson to take a DNA sample to send to the lab.
Pruett is handed over to the military where they want to seek the death penalty in order to sweep the criminal and the crime under the rug. The military court calls Benson to the stand to talk about her investigation into Jessie's rape and murder. She discusses Jessie's history and brings up that she was pregnant with her rapist's baby, and that they have Pruett's DNA sample to link him to the umbilical cord that was attached to the baby.
Fin tells Benson that the secret about her being in counseling is safe with him, and assures her the flashbacks will go away. Cragen interrupts their conversation to tell them that Pruett's DNA does not match that from the baby's umbilical cord. Benson's stomach sinks as she realizes Pruett was telling the truth and he really wasn't Jessie's rapist. Benson is back to her four other suspects.
Benson turns her attention back to Gary, the higher-ranking man with aggression issues. Benson talks to Gary's wife and accuses her of helping Gary cover up his crime so he would keep his pristine position with the military. She refuses to believe the news that Gary's DNA matched the baby's umbilical cord. Benson offers the wife a deal and she starts talking.
Gary's wife says she never meant for Jessie to end up dead. She was hurt when her husband admitted to "having sex" with Jessie, and Jessie was going to tell the truth and say he raped her. So she reached out to Jessie and said she was sorry for what Gary had done and she needed Jessie's help to protect her own family from him. Jessie agreed to meet with her, which is how Gary was able to find out where Jessie was and silence her forever. He also took the only evidence tying him to the crime, his baby, and threw it into the Hudson river.
After Benson gets her confession and closes her case, Cragen calls her into his office. He tells her they found Jessie's baby boy in the river. Benson is heartbroken. Before she can leave, Cragen orders her to take some personal time off. When she asks if it's an order, he says no, because then it would have to go in her files. He tells her to take as much time as she needs to heal.
Pruett is cleared of all murder charges based on Gary's guilt. Before he can leave, Benson wants a chance to apologize to him. He tells her the job was to find justice for Jessie and she did that. Benson thanks Pruett for being the one friend in the military that Jessie could have trusted. He said he would have gone to his superiors, but Gary had already turned him in for fraternizing with Jessie off-hours on the camp, and it would have looked like retaliation.
Benson confesses to Pruett the real reason she held a gun to his head the day she broke up his and Gary's fight. She admitted she was a victim of sexual assault as well, and the fight triggered flashbacks for her. He tells her she needs to realize she is not the one to blame. He looks her in the eye and tells her it will take practice, but she will get there. As he leaves, she tells him to be careful while heading back to the service.