The fugitives are ambushed by a troop of gorillas. After a tremor and avalanche stops their captors, they scramble over a hill to find themselves in the ruins of San Francisco, once the home of Alan Virdon. A second earthquake knocks Burke and Galen unconscious and when they wake in a cell, Virdon is nowhere to be seen. Outside, they hear a gunshot and voices talk about 'removing the carcass'. The door opens and Burke is removed to be interrogated by armed humans. They refuse to believe that he would willingly travel with an ape. Galen, meanwhile, is tortured by his guard. Burke makes a break and runs out into the ruined city. The humans begin to fire on him, when one of Urko's gorillas appears before them. When Burke stabs the gorilla to death, his human pursuers welcome him into their ranks.
In Central City, Galen's father, Yalu, tries to persuade the council to allow Galen to return to his home without penalty, as his mother is dying. Despite Urko's objections, Zaius believes that the best way to stop the trio spreading their dangerous ideas is by revealing that it was Galen's idea to leave his human companions. As Burke is taken to the human headquarters on Alcatraz, he asks his new comrades to keep Galen alive, and is surprised to hear that they have no knowledge of Virdon - he was neither killed nor captured. Urko, having assembled 500 gorilla soldiers at the edge of the city, orders an attack and the capture of Galen - alive. The humans fight hard but are driven back towards their fort headquarters.
- The story remains unfinished. The next issue was to begin 20 years on in a battle scene where an ape military leader commands his troops. It would be revealed that the ape is actually a bitter old Galen, turned against humans after the death of his mother and the slaying of his close friend Pete Burke. Urko was unhappy with Galen’s return to Central City, and the two feuded. Urko plotted to murder Galen, failed, then killed Galen’s father. Urko was many years older, and what Galen lacked in physical strength was more than compensated by the technological marvels he had discovered from the planet's past. Galen got his position by murdering Urko, and has been leading a devastating army of apes trained to kill all humans. Meanwhile, Alan has been located by his son and another two astronauts. Alan has been told his friends are dead and only discovers Galen is alive in a tragic and dramatic conclusion.