They arrive in Beacon Hills at the end of Scott's sophomore year and lure Boyd and Erica to them, capturing Isaac later in the summer. Braeden helps Isaac escape and he tells Derek that Erica was killed but Boyd and another girl are still there. When Scott and Derek break in, they realize that the other girl in Cora, Derek's long lost sister. The Alpha pack wants Derek to kill off his betas and join them (there's a pole shoved through his ribs during this speech), and after they leave Derek kicks Isaac out, not trusting his own resolve.
When a meeting "just to talk" goes terribly wrong, it appears that both Derek and Ennis are killed, and a combination of stress and guilt keeps Scott's wounds from healing. In reality, Ennis could have been saved by Deaton although Deucalion decides to kill him, and Derek is somehow alive enough to get to Jennifer Blake. While Aiden was suspended form school at the time, Ethan attends the cross country trip with Scott, Stiles, Boyd, and Isaac, and Isaac ends up attacking him. Later at the team's motel, Stiles stops Aiden from committing suicide due to wolfsbane posioning, and in return tells Scott and Stiles that Derek probably isn't dead, but if he hasn't joined their pack by the full moon he will be. Later in the week there's another fight in Derek's loft and Kali and Aiden use Derek to kill Boyd. In the flashback episode, Visionary, Gerard Argent gives Scott and Allison a basic overview of how the history of the alphas in the pack is connected to the Hale history. Deucalion was once a very progressive Alpha who believed in compromise and discourse before Gerard took his sight.
The Alphas have little relevant action in the next episode because it is revealed that Jennifer Blake is the Darach, but in 3x10 there is a showdown in the hopsital. Their goal is to simply get Jennifer, but Derek is keeping Jennifer at his side because she can help Cora, also revealing that the Alphas actually want Scott, a True Alpha, not Derek. Deucalion goes to Melissa McCall and has her shut off the backup generator at the hospital. Kali says that Jennifer Blake was once her emissary, and she originally decided to let her die from her wounds so she could die in peace, but Jennifer found the Nemeton, powerful from Paige's death there, and ended up not dying. When Jennifer kidnaps Melissa, Scott decides to side with Deucalion so he can get his mother back.
After Scott, Allison, and Stiles' sacrifice, mentions his deal with Deucalion, which he created because they probably can't beat Jennifer without him. Ethan goes to the loft where Derek, Peter, Lydia, and Cora are and tells them that Kali and Aiden are on the way. By the time they arrive Derek and Cora have left. Jennifer comes through the glass ceiling next, killing Kali and disabling Ethan and Aiden. Scott, Allison, and Isaac meet up with Deucalion and Allison and Isaac go to the root cellar while Scott and Deucalion wait for Jennifer to show up. She does . . . with Derek. Cora and Lydia bring the twins to Deaton, who starts to take care of them. Under Derek's persuasion, Jennifer heals Deucalion's eyes so that he can see the price she paid for Kali to join the pack. Deucalion's powers return when the eclipse ends, and he slashes Jennifer's throat. Derek and Scott decide not to kill Deucalion as long as he leaves and lives as the man Derek's mother knew. Aiden and Ethan stay in Beacon Hills for Season 3B, but no longer as a pack.