As the maggot approaches Jo, Hinks breaks in. The maggot turns and attacks him then crawls away. Hinks quickly succumbs to the green death as the Doctor scrapes up some slime for analysis.
In the morning, the Brigadier prepares to destroy the minhead and seal it off.
As Cliff examines the green slime destroying human tissue, the Doctor decides to get another maggot. But hearing of the mine's destruction, he confronts first the Brigadier, then Stephens. He accuses Stephens of trying to cover up what his waste is doing to the mine and Stevens threatens to have the Doctor arrested under his emergency powers. He bring in a man from the Ministry – Mike Yates. As the Doctor argues with him, time runs out and the Brigadier seals the mine – over the protests of Cliff and Jo. The Doctor storms out of Global Chemicals. The Boss warns his "little superman" that their day is approaching.
The Brigadier is convinced that the maggot problem is solved. But a cleaning lady is working in the pump room at Global Chemicals when she sees giant maggots squiggling around in the pipe. Benton and the soldiers see maggots crawl out of the ground near the mine.
Elgin is shown the maggots and goes to Stevens. Stevens wants to simply flush more waste down the pipe but Elgin is ready to blow the whistle. Stevens and the Boss subdue and process him.
The Doctor, Cliff and Jo work on a aoslution and worry what the maggots are going to molt into. UNIT tries armor-piercing bullets and pesticide on the maggots with no success. The Doctor believes they need a biological weapon but they need more samples for experimentation.
The Doctor has the Brigadier ask Yates to get more oil waste from Global Chemicals. But Yates is under constant supervision. The Doctor offers to break in but is warned that security has been doubled. The Doctor then takes a milk truck, dons a disguise and drives into the factory.
Jo is working with Cliff and knocks some brown fungus onto his slides, infuriating him.
Alarms ring out in Global Chemicals. The Doctor hides in a closet and begins to change.
Jo tries to talk to Cliff and he sarcastically suggesting she make some tea. Frustrated, she scribbles a note and stomps out.
Yates is leaving when he passes the Doctor dressed as a cleaning woman. He evades the guard and joins up with the Doctor.
Jo arrives at the pit with a cage and pretends to be looking for the Doctor.
Yates is convinced Global Chemicals is responsible for the problems but can't get any waste or the formula. He has learned of a special lift to the top floor and believes Stevens is taking orders from someone there.
Cliff happens to look at the slides Jo spilled the fungus on. To hs delight, he finds that it's killing the green slime. He then finds her note and races to the pit.
The Doctor uses his sonic screwdriver to break into the special lift. The Boss's voice greets him as he steps out into a gleaming room filled with computer equipment. The Boss is not a man — BOSS is a computer!