The ALA attacks New York City, killing several people in a bombing. When news about Charlie's past ties to the ALA resurfaces, the town grows suspicious of his terrorist connections. Unfazed, Charlie goes to school as usual, not realizing what the ALA has in store for him as a mysterious man approaches Lucy.

Lucy visits Eva, the chimpanzee who gave birth to Charlie, at The Kornberg Primate Research Institute. There, she meets Dr. Fowler who tells her a few secrets about Charlie's birth. She later joins Charlie's family for dinner as Hannah celebrates Charlie's first friend, unaware that the ALA members are lying in wait.

Charlie suddenly goes missing. While Bert and Hannah search everywhere for him, Charlie is calmly confronting Rivera, Lippman and Min-su of the ALA. He gives them an ultimatum and things seem to be heading towards a peaceful conclusion until Rivera makes a drastic move.

Charlie is finally released from custody with the help of Congresswoman Dafne M. Linares, who ran on the platform of animal rights. When he returns to school, however, the warm reception he once received is now replaced with scorn and slander. Despite all this, Lucy takes steps towards getting Charlie his civil rights.

Charlie goes viral once again for stopping a fight between Ozzy and student activist Gare. Instead of thanking him, Gare questions why Charlie is not more passionate about animal rights. Disappointed with Charlie's stance, Gare livestreams about feeling powerless as an activist when he receives a mysterious invitation.

Students panic and the world watches in horror as a masked man livestreams himself shooting students in Shrews High. Deputy Philip Graham storms into the school, but is shocked to find Charlie trying to save the wounded. Meanwhile, Lucy comes face to face with the shooter as he prepares for one final and very public message to Charlie.

Public anger over the school shooting leads to a growing number of attacks on vegans and activists nationwide. As anti-ALA sentiments intensify, misinformation about Charlie protecting the shooter raises suspicions about his terrorist connections, leading to a confrontation with the townspeople.

Lucy runs into Deputy Phil and tells him the truth behind the pool incident ten years ago. As Phil questions his own opinion of Charlie, Hannah senses something has changed in her adopted son. That night, Lucy and Charlie exchange messages as usual. However, Lucy's unusual response raises Charlie's suspicions.

Charlie goes alone to save the kidnapped Lucy. After confronting the armed ALA members, Charlie finally finds Lucy with Rivera. Delighted to meet him in person, Rivera tells Charlie the truth about the ALA raid that rescued Eva fifteen years ago and its connection to Dr. David Grossman, Charlie's biological father.

Charlie returns after rescuing Lucy to find his home engulfed in flames. He rushes in to save his parents, but it is already too late. Realizing their deaths are suspicious, Charlie quickly disappears into the woods to evade police capture. A manhunt ensues as the authorities discover that Rivera has also gone missing from custody.

After losing his parents, Charlie is adopted by Deputy Phil and his wife Grace. They start a new life together despite the media frenzy and Phil's suspension for choosing to protect Charlie. However, more change is on the horizon for Charlie as his latest medical exams indicate his body is undergoing a transformation.

As Charlie tries to return to a normal life, the nation is horrified to learn about the ALA's latest atrocity. Charlie seems to pay it no mind, though, and makes a visit to his biological mother Eva, who is on her deathbed. When Lucy finds a way to help Eva communicate, her final message for Charlie leaves everyone in shock.