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With Fisk behind bars, Hell's Kitchen is caught in a gang war, and someone is solving the problem in the most violent way possible. Entire gangs turn up dead, and the press calls the shooter the Punisher. He's Frank Castle, a former Marine whose wife and kids were killed in a gang shootout in Central Park. Matt faces Frank on a rooftop and ends up chained, listening to him argue that killing is the only answer. The question hangs over the whole season: what's the difference between them?
Frank is arrested, and Nelson & Murdock take his defense in a trial that turns into a circus. Karen digs into Frank's family and learns that District Attorney Samantha Reyes knew about the shootout and covered it up. At the same time, Elektra Natchios, Matt's rich and dangerous ex from college, comes back. She drags him into an investigation of Roxxon and the Yakuza, and Matt spends his nights with her, skipping work and the trial.
Behind the Yakuza is the Hand, the ancient organization Stick fights. Nobu, who seemed dead, is back. The Hand digs a massive hole under the neighborhood and keeps young people locked up on a kind of farm, draining their blood. Elektra kills to get things done, and Matt can't accept it. In court, Frank sabotages his own defense and goes to prison. There, Fisk uses him to kill a rival and then helps him escape. The firm falls apart: Foggy and Matt fight, Karen pulls away, and the partnership ends.
Frank learns the man responsible for the shootout that killed his family is someone called the Blacksmith, who runs the heroin trade. Reyes is murdered. Frank tracks the Blacksmith down, Colonel Schoonover, his old commanding officer in the Army, and kills him. Meanwhile, Nobu reveals that Elektra is the Black Sky, a living weapon the Hand worships. Stick tries to kill her, but Matt stops him.
On the final rooftop, Matt and Elektra fight the Hand together. Frank shows up with a rifle and saves them both. Elektra steps in front of Matt and is killed by Nobu. Matt reveals to Karen that he's Daredevil. Foggy goes to work for Jeri Hogarth, and Karen becomes a reporter. Frank burns down his old house and fully takes on the Punisher name, holding a mysterious disc. In the last scene, the Hand digs up Elektra's body and places it in an ancient sarcophagus.