Starting moments after the the previous episode ended, "End of Days" begins as Buffy (Sarah Michelle Gellar) effortlessly pulls the scythe from the stone. The First tells Caleb (Nathan Fillion) to let Buffy go, so that she could attempt to save the Potentials from the trap Faith (Eliza Dushku) led them into. Meanwhile, in the sewers, those that survived the bomb blast are dragging the wounded to the surface when they are ambushed by three Turok-Han vampires. Buffy arrives in time to kill the vampires with her new weapon.
Back at Buffy's house, the Potentials and Faith pledge their loyalty to Buffy again, while Willow (Alyson Hannigan) and Giles (Anthony Stewart Head) search the Internet for references to the scythe - finding a connection to Ancient Egypt. Faith and Buffy bond over their shared loneliness as Slayers, and reflect how they are the only ones in the group who truly understand what it feels like to be a Slayer. Buffy admits to Spike (James Marsters) how special the night they shared was and that it gave her the strength to find new courage. Spike tells Buffy that it was the best night of his life.
At Buffy's insistence, a reluctant Xander (Nicholas Brendon) renders Dawn (Michelle Trachtenberg) unconscious with chloroform and drives off with her, away from Sunnydale for safety. When Dawn wakes up, she gives him a shock with a stun gun and then drives them back.
Following the Egyptian lead, Buffy takes the scythe to a small pyramid outside the gates of the same cemetery that she has patrolled for the past six years. Inside, a woman who claims she is part of a secret female order that has watched the Watchers since ancient times tells her that the scythe is a powerful weapon forged for the final battle. Suddenly, Caleb shows up from behind the woman, kills her, and almost has Buffy bested when Angel (David Boreanaz) steps in to save her. However, Buffy insists on fighting Caleb alone, and Caleb falls.
Buffy gives Angel a welcome kiss. Unknown to them, Spike is watching them from the shadows with the First, in the guise of Buffy, by his side. "That bitch", it tells him.
This is the first time that Angel and Buffy have seen each other since their off-screen interlude after her return from death, between Buffy episodes "Flooded" and "Life Serial", and Angel episodes "Carpe Noctem" and "Fredless". They were last on screen together in "Forever".