The third episode of Helix picks up right where the second left off. Day 3 begins with Alan finding his ex-wife Julia passed out on the floor of the shower after being attacked by Alan's infected brother Peter. Julia tells him that she doesn't remember what happened to her and she's just overworked. Alan goes to wait for her in the hallway when he hears something bump in the air vents. When he follows the sound to a lab Peter drops down behind him. He surrenders himself then passes out.
Sarah and Doreen are watching over the scared locals, one vest wearer in particular speaks up, which means he promises to be a troublemaker later on. Behind the glass Daniel, Hataki and Balleseros are watching and discussing recent events. Daniel says they are still looking for the three people who escaped the day before and Balleseros reveals that two more people have become infected. Then Alan wheels Peter into containment.
Hataki is worried that Peter will escape again, so he suggests putting him somewhere more secure. Daniel gives Alan and Balleseros a tour of a lower level that was abandoned years ago. It has since been used for dangerous experiments, including nuclear research. When Daniel confirms that the area has been tested for radiation Alan says that he wants to turn the floor into an isolation area for normal infected and vectors, which is the name given to those like Peter who are actively trying to spread the virus.
After a scene of Julia struggling with her denial that she is infected we return to the group returning from the abandoned area. As they walk and talk they come upon escapee Dr. Sulemani, whose infection has worsened. She walks towards Hataki until Daniel shoots her. After Alan saves her life, he berates Daniel and insists that there is no more lethal force.
Alan gets his team together and assigns Julia and Sarah to create a test and Doreen will continue her work with the monkey, which is the best chance for a vaccine.
When Doreen and Balleseros return to the lab they find that the monkey has been stolen and all traces of him have eliminated. Balleseros promises Doreen another sample to keep her from going to Hataki, so he takes her to the frozen monkey graveyard. She becomes aggressively suspicious, so he tells her that he thinks Hataki intentionally caused the outbreak.
After monologuing to unconscious Peter about how he saved her from her boring life with Alan, Julia returns work in the lab with Sarah. Once Sarah develops a test she goes to tell Alan, leaving Julia to use the test on herself, which comes up negative.
Alan and a security team confront the second escapee, Dr. Bryce, who is taking an ax to a door because he says there is a cure on the other side. When Alan asks Hataki about the cure he says they were working on a single cure for all diseases, but it was successful on 25% of the time and killed the rest.
Doreen gives the new monkey sample a growth factor, which causes a black substance to grow uncontrollably. Balleseros tells her to keep it a secret from everyone so Hataki doesn't find out and repeat the monkey theft.
When Daniel arrives to take Sulemani to the isolation floor she tackles him and runs away. Daniel tells Julia what happened and that she killed Bryce. Vest guy overhears and starts a riot. Sulemani brutally attacks a security guy. As Julia stares at the woman eating a man's face she finally accepts the reality that she is infected. Then Sulemani makes eye contact with Julia and runs at her. TWIST! Alan shoots Sulemani because he still cares about Julia. Julia tells Alan that she is staying in isolation.
Back upstairs Alan says the isolation level should be sealed off. He admits that he has lost control of the situation and he will call the army for backup when the comm link is up.
In her bedroom, Sarah's hand continues to shake,she takes a pill and removes her shirt, revealing a big mysterious scar going up her back.
In isolation Julia realizes that the test doesn't work. While she's on the phone with Alan, someone in camouflage, presumably Balleseros, blows up the communications satellite.