Scott, Allison, and Stiles wake up in tubs in a long white room. They walk to the other end of the room where the trunk of a tree juts out from the ground. The tree trunk is the Nemeton. Scott leans over to touch the center and he is suddenly in a forest. He is having a third-person flashback to when he was first attacked by a werewolf. He backs up into the Nemeton. Stiles and Allison also flash back to that same time. Allison gasps for air as she lifts her head out of the ice water.
All three of them wake up in their ice water baths and say they all know where the Nemeton is. Dr. Deaton tells them that they were underwater for 16 hours and the full moon is going to rise in four hours.
Cora pours water into Derek's mouth. He is glad to see that she is okay. Cora says that it's all thanks to Derek giving up his alpha powers to save her. Peter warns Derek that he only has a few hours to prepare himself against an alpha werewolf, who wants to tear him apart.
Scott feels that Deucalion can't beat Jennifer without him. Stiles, Allison and Isaac try to convince him not to go but Dr. Deaton thinks Scott may be right. Ethan shows up looking for Lydia because he wants her to help him get his brother back.
Jennifer's victims lose hope about escaping from the root cellar they are tied up in. A strong wind starts to blow above them outside.
Ethan warns Peter that Aiden and Jennifer are coming for them. Peter wants Derek to run but he doesn't think he will lose against them. Peter asks how Lydia feels about it and she says she feels like she's in the middle of a graveyard. Peter warns Derek to get at least 100 miles away to be sure he's safe.
Scott, Isaac, and Allison head to her house to find clothing with her father's scent on it. In her father's study, Rafael, Scott's father who is an FBI agent, waits with two police officers. He wants to know what is going on and hopes he won't have to arrest his son. However, he will stay all night long if that is what it takes to get answers.
Kali asks Lydia where Jennifer is. She doesn't know though and Aiden growls at Kali. Lydia comments that she thinks it is about to get violent when Jennifer drops in through the ceiling. She asks who wants to go first and fights Kali, Ethan, and Aiden. She quickly subdues them and then shows Kali her true power. She levitates glass shards and throws them at Kali, killing her. As Jennifer turns toward Lydia, Ethan, and Aiden join to form one huge werewolf but Jennifer easily snaps their neck and they die.
Stiles drives his car through the storm but gets into an accident.
Back in her father's office, Allison points out that her father is licensed to sell weapons. She describes various guns and then creates a diversion by tossing a smoke grenade. She runs out of the house with Isaac and Scott. After they escape they wonder where Stiles is, but they can't wait for him.
Jennifer wants Lydia to do what she does best, scream. Jennifer shows her true form which causes Lydia to scream. Derek, driving away with Cora, hears Lydia's screams and says they have to go back.
Scott, Isaac and Allison meet with Deucalion on the top of a hill. The others aren't there so it will be just Deucalion and Scott against Jennifer. Scott tells Isaac and Allison to get Stiles and bring him to the cellar to help free the captives. He has a plan to keep Jennifer away from the cellar.
Derek meets with Jennifer, who tells him that if he becomes her guardian it will save the three parents she has captive. Or she can use them to be her guardian. Jennifer says she doesn't have a chance against Deucalion and Scott unless Derek helps her. If he helps to kill Deucalion, the others will live.
Isaac and Allison find the cellar near the Nemeton. The ground around the tree begins to cave in.
Cora tells Lydia that they need to get out of there. They hear the twins separate and Lydia is surprised to find them alive.
Deucalion asks Scott about his plan. He sends Jennifer a video text about where to find them.
Allison and Isaac untie the captive parents but their escape route is blocked by debris caused by the collapsing cellar. Isaac holds up the ceiling to save the others.
Cora and Lydia bring Aiden and Ethan to Dr. Deaton. He says that they can only be saved if they start healing on their own.
When Jennifer and Derek arrive, Scott asks what Derek is doing there. He tells Scott that he is actually helping him. Deucalion taunts Jennifer and the things she had to do to gather enough power to face him. Deucalion and Derek transform and fight each other. Jennifer tries to use her magic on Deucalion but it does nothing. He takes both of them out with ease. Deucalion tells Scott to kill Jennifer and growls, causing Scott to transform. Jennifer says that even if he kills her, Deucalion will have him kill everyone he loves. He tries to force Scott to kill Jennifer, but Scott throws two flashbang arrowheads down and blinds Deucalion. Everyone returns to human form as the eclipse starts. Jennifer is gone.
Isaac has almost lost his grip on the ceiling when Stiles shows up and uses a baseball bat to hold it up.
Jennifer returns in her true form and bashes Deucalion's head into the ground repeatedly. Derek urges her to stop and heal Deucalion's blindness so that he can see the price she has paid to get her power. She heals his eyes but it causes her to lose her power for a few minutes, just like Derek lost his after healing Cora. She asks Derek to kill Deucalion for her but he refuses. He is a predator but he doesn't have to be a killer. He tells her to let her prisoners go but she punches him away.
The shadow has passed over the moon and the werewolves regain their powers. Jennifer throws down a circle of Mountain Ash and says she will soon have enough power to defeat them. Scott attempts to enter the ash circle. His eyes turn from yellow to red while Jennifer looks increasingly worried. Scott enters the circle and knocks Jennifer down. Deucalion and Derek have looks of amazement on their faces. Scott asks Jennifer to stop the storm and save her captives or he will kill her. Deucalion walks up and slits her throat.
The storm is over and those in the cellar are safe. Derek and Scott allow Deucalion to go free, hoping that he will once again be a man of vision.
Allison's father packs up his weapons to put in storage but Allison has another plan. Dr. Deaton says that Beacon Hills may become a beacon for creatures and she thinks she should be prepared to battle them. She wants their new code to be "We protect those who cannot protect themselves."
Scott says that he and Stiles both feel darkness everyday but he looks for his friends instead. Dr. Deaton asks Scott what happened to Jennifer after the fight. He doesn't know though, her body was gone when they went back.
Jennifer crawls to the Nemeton and begs for it to save her, but Peter stops her. She says that he will try to steal alpha from Scott. He slashes Jennifer's throat and screams that he is already the alpha and always has been.