With Constance Sutton gone it's just a normal day at the office for the cast of Helix.
Sarah starts Day 9 by playing bait for a hungry vector. She walks down a hall in Level R, minding her own business when her target comes out and chases her. She jumps behind a gate and Daniel's security team tases the vector. Alan points out that Level R is completely abandoned and inspects the vent that the vector came out of. He notices that air is coming up even though they were told there is nothing below them.
Hatake reveals that the secret basement is called Level X and it holds all of the original virus samples. He explains that he was tasked by Ilaria to create a doomsday virus and uses the "if I didn't do it someone else would have" excuse. He warns that Constance was nothing compared to the army that Ilaria is sending.
Julia asks Hatake about the picture of the two together when she was a child. He tells her that he was a friend of her mother's but leaves out the part where they made a baby together and it's Julia.
Miksa, formerly known as Daniel, explains that Level X is a 150 year old Russian trading post. He pulls up a security camera to confirm that the vectors are down there. Alan asks how they will get down to destroy the core virus that started everything. Hatake says he will go through his secret staircase. Alan doesn't trust him so he promises to come up with a different plan.
In Level X the vectors spit blood into Hatake's "Keep Calm" mug and pour it into Peter's mouth. He wakes up and rises above the crowd. They are at his command and respond to his every motion.
Alan talks with the cryogenics specialist Dr. Adrian, who puts the freshly caught vector on ice. Alan says he will bring the cold from outside to the vectors inside.
Constance's right hand man Lt. Klein is thrown in a cell with Balleseros. Klein tells him that Constance sent a team to kill Anana and burn the whole village.
In a heist style scene Alan tells his plan to destroy the core sample. He and Julia go to Level X, Sarah and Hatake turn the power off thus letting the cold in and freezing the vectors, while Miksa/Daniel and his team pass out blankets and keep the civilians warm.
On their way to Level X Alan tells Julia that if the plan doesn't work they will have to burn the base and kill everyone. They find the vectors frozen solid and make their way to the store room. They find more viruses than they expected and try to destroy all of them.
Back upstairs, Sarah enters a trance like state and gets very personal and a little existential with Hatake. He realizes that she has a tumor when she has a seizure so he turns the power back on ahead of schedule.
Balleseros takes advantage of the power outage to escape from his cell. Once out he kills Klein. Miksa/Daniel finds the body and goes after Balleseros. He catches him getting on a snowmobile and learns that Anana is in danger, so they both go to her rescue.
Julia and Alan realize that the sample they went down there for is missing just as the vectors slowly begin to wake up. After getting past the vectors Julia sees another set of her initials written on the ground by a hole. She and Alan go down to the secret level under the secret bottom level. They find Julia's childhood home.
Anana finds her brother and Balleseros looking for her, and joins them to save the village. They find Constance's men herding the people together to burn them so Anana pretends to be a prisoner so they can get close. Miksa/Daniel meets his twin for the first time and punches him. The Ilaria people are about to kill Tulok but Daniel takes the gun to do it himself. Then he, Balleseros, and Anana turn on the Ilaria men and kill them. Everyone is saved and Tulok gets back at his brother.
Julia and Alan get up from the secret house and are greeted by Peter and his posse. Julia tells Alan to stay behind her and she leads the way as the vectors stand helplessly by. They arrive to find Sarah unconscious with Hatake sitting over her. He tells them about her tumor and Alan takes her to the ICU for surgery. She wakes up some and babbles, letting slip in front of Julia that she and Alan slept together.
Julia asks Hatake about their relationship. He shows her the torn picture of the two together and says it was one of the happiest days of his life. He then adds the other half of the picture that shows Julia's mother, Jane who died when her daughter was very young. Julia recognizes her as the hallucination Jaye. Hatake reveals that all of Julia's memories of Montana actually occurred at the base. He removes his contacts and says "you have your father's eyes".
Miksa/Daniel spends time with his family reminiscing. He remembers fighting with Tulok over a Hot Wheel with butterfly doors. Balleseros enters but stumble because he is still weak from the pick ax.
The episode finishes with a montage set to Michael Andrews and Gary Jules' cover of "Mad World". At the end of it the cryogenics specialist Dr. Adrian is revealed to have the core virus.

image courtesy of Syfy/NBC