The Brigadier give the Doctor a rock covered in green slime as source material. The Doctor is still puzzled by Cliff's delirious ravings about serendipity.
Benton then brings in the ruptured husk of a maggot - they are beginning to hatch. Just then, Nancy sees a maggot in the kitchen. But it has died after eating a fungus roast.
Stevens and BOSS are hard at work on their plans. Stevens wants to eliminate Yates but BOSS decides to give him the total processing which will make him the first of the slave elite.
The UNIT soldiers pile sacks of brown fungus into Bessie. The Doctor and Benton drive to the mining pit where Benton starts throwing it to the maggots, who eat it and begin to die.
The green glow begins to spread further over Cliff's body. Stevens takes Yates to be processed, but Mike breaks free and escapes.
As the Doctor and Benton continue to destroy the maggots, a massive green fly attacks, spraying green slime at them. The Doctor throws his coat up into the air and the fly crashes into it.
Jo tells the Doctor that she had an accident in the lab, spilling fungus over Cliff's slides. The Doctor figures out it is the same fungus that killed the maggots.
The Brigadier sends Mike to the Doctor with his report on BOSS's plans. Nancy finishes the cure while the Doctor returns to Global Chemicals.
Stevens begin the countdown to activation.
The Brigadier and the Doctor reach Global Chemicals but the guards won't let them in. The Doctor heads in alone but tells the Brigadier to destroy the factory and BOSS if he doesn't return by 3:57.
BOSS is mad — singing as his plans come to fruition. He activates the processing of the slave elite, causing the gate guard to freeze. The Doctor rushes past the motionless guard.
Stevens continues to work and puts on the processing headset.
Jo and Nancy swab a brown liquid on Cliff's neck. He immediately begins to recover before Jo's affectionate gaze.
The Doctor reaches the computer room. But Stevens no longer exists, having been taken over by BOSS. The Doctor tries to wake Stevens, telling him their glorious plan has produced only evil. He uses the blue crystal to breaks Stevens' conditioning.
Stevens tells the Doctor to leave and begins cross-feeding the generator circuits to blow up the factory. Despite the rantings of BOSS, he finishes the job and slumps into his chair, crying. The Doctor escapes just before Global Chemicals goes up in a tremendous explosion.
Cliff is completely restored. The Doctor wants to return to UNIT but Jo tells him she's decided to go with Cliff to the Amazon. Cliff casually suggests they get married and Jo happily agrees.
Jo has a tearful farewell with the Doctor. He gives her the blue crystal as a wedding present. As the Nuthatch and UNIT people toast the couple, the Doctor drains his glass and quietly leaves, noticed only by a conflicted Jo. He takes one last look back and drives off alone into the Welsh evening.