The first season finale of Helix begins with a flash forward to a year after the pilot.
Alan is shown torturing a male immortal to find out where Julia is. Back in the present he holds her back when she is tempted to the same to Spencer, who cut off her finger and strapped a bomb to her neck, to find her mother. She then goes to her weeping father. He tells her that Daniel sacrificed himself for her because he knew Hatake would have chosen Julia over him anyway. He admits that his daughter by birth is more important to him than his adopted son which is maybe the most messed up thing Hatake has done, and he invented a doomsday virus. He adds that he knew her mother was alive because Ilaria was keeping her hostage to force him to make the virus and he didn't tell her before because he didn't want to give her false hope.
In the basement Sarah prepares to leave the extras to look for Alan. She has another headache and Dr. Haven is concerned. He studies Sarah's blood and says she is showing signs of cancer. She runs away before he runs more tests because she is a scientist who doesn't understand how immortality works.
Alan and Peter go back to Spencer and offer to trade his freedom for Julia's mother. Again Alan restrains someone from torturing the boyish assassin. Spencer tells them they are too late to stop the virus and shows them a news report of an outbreak in Lares, Puerto rico. Alan assumes that Balleseros is behind it.
Balleseros faceplants in the snow. Anana and Tulok are looking for him and find his abandoned snowmobile. Tulok wants to stop the search but Anana insists they continue because it;s what their ancestors wanted or something. Balleseros wakes up face to face with Spencer's lacky Blake. He slept with her and didn't call her and that's super important to the story. She tells him she has the virus and the cure.
Peter points out that the virus is not creating vectors in Lares, indicating that Ilaria is using the isolated city as a test. Julia, Alan and Hatake go after the virus and Julia's mother while Peter is left to guard Spencer. When they get there Balleseros has knocked down Blake with the gun she gave him which is now aimed at the most dysfunctional family on TV this side of Westeros. He shoots Blake and insists he is not working for Ilaria. He wants the list of children taken by Hatake and doesn't know anything about the outbreak. Hatake agrees to write down the list of children, which he knows by heart, in return for the canisters holding the virus and cure.
Julia frees her mother from the box, but she doesn't recognize her daughter at first or realize how much time has passed. After Julia talks with Alan her mother regains her lucidity. She says she stayed with Hatake as as long as she did because she loved him and hoped he would change. Soon after, Hatake enters and kisses her.
Spencer taunts Peter and says he is stuck in Alan's shadow. Peter puts a knife to the assassin's throat but then uses it to cut his bonds. Apparently Peter has been working for Ilaria for years and it was he who unleashed the virus on Lares. He gives Spencer the trigger for the bombs Hatake planted on the base.
Anana and the villagers arrive as Balleseros is preparing to leave. They brought enough snowmobiles for the base to be evacuated. Alana and Tulok are told of their brother's death. Peter stumbles in and warns that Spencer "escaped." Hatake tells Alan that Spencer has one weakness.
As everyone prepares to leave the base Alan gives the canisters to Julia and the two kiss as Peter watches from afar. Haven comes to Sarah to tell her she is pregnant which only seems like a spinal tumor to two highly educated scientists. This show is about scientists.
The doors open and reveal Spencer, who sets off the bombs. When Alan comes to he sees Spencer holding his blade to Julia's throat. He says his people have been persecuted for centuries. Julia's mother tells Spencer that his parents were filthy liars. He kills her because she addresses him by his name. He takes Julia to the helicopter and Alan throws his mother Constance's severed head on board. He climbs in while Spencer is distracted. Julia gives Alan one of the canisters and pushes him out of the aircraft.
Back in the future Alan relaxes at a French café after a long day of compromising his values by torturing people. He reads a French newspaper with Narvik in the headline. The waiter slips him a card with the Ilaria logo printed on it. He makes an X on the wall behind him in chalk before meeting with Peter in an alley. He tells him Julia is alive and to proceed without him if he isn't at the checkpoint. He looks up at a building with the name Ilaria on it. Inside several silver eyed people sit around a meeting table with Julia at the head and a prosthetic finger on her hand.

HELIX -- "Das L'ombre" Episode 113 --Pictured: (l-r) Hiroyuki Sanada as Dr. Hiroshi Hatake, Kyra Zagorsky as Dr. Julia Walker, Billy Campbell as Dr. Alan Farragut -- (Photo by: Phillippe Bosse/Syfy).