The home of young scientist Eugene Whitlock is invaded by the Thought Police. For breaking every law of the High Tribunal, Whitlock is sentenced to death. A flame thrower sets him and his house ablaze.

Outside the burning home, Morlock has transformed once again into a mindless Plant Monster. The Thought Police are devoured by Morlock as they attempt to flee the burning house.

Meanwhile, inside the house, Eugene Whitlock still lives despite suffering 3rd degree burns over his entire body. Incredibly, he feels no pain. As he attempts to leave the burning wreckage, he encounters an unconscious Morlock, who regained his human form.

Whitlock realizes that this is the fugitive Morlock wanted by the Thought Police. He takes Morlock to the Emergency Underground Railway, where they are transported to the Great Refuge.

Whitlock has now named himself the Midnight Man. He vows to form a revolutionary army and overthrow the High Tribunal. Whitlock also claims to be able to cure Morlock of his transformations into the mindless plant monster and in turn increase his powers.

But before the plans can come to fruition, the Great Refuge is invaded by the Thought Police. The battle triggers a change in Morlock. He begins to transform into the savage Plant Monster.

With the Refuge under attack and Morlock about to transform, Whitlock has no choice, he shoots Morlock and decides to destroy the Refuge, taking the Thought Police with him. Is this the end of Morlock and the Midnight Man ?