In the Welsh village of Llanfairfach, the local colliery is closed, and the out of work miners are protesting outside the factory complex of Global Chemicals. Nothing Stevens (Jerome Willis), the chief of Global Chemicals, can say will calm them. 

A miner, Ted Hughes (John Scott Martin), returns from the disused mine and sounds the alarm. When he is found, he is dead, and glowing bright green. UNIT are called in to investigate and to provide protection for Global Chemicals. Jo decides to join Professor Clifford Jones (Stewart Bevan), a Nobel prize winning ecologist, and his group at The Wholeweal Community - known locally as 'the Nuthutch'. They are concerned at the pollution resultant from Global Chemicals' processes. The Doctor, however, makes a trip to Metebelis 3. 

Stevens explains to the Brigadier (Nicholas Courtney) that their processes create no pollution or waste, but Cliff tells Jo that this cannot be the case. Jo guesses that they must be pumping the waste down into the old mine-shaft. She decides to investigate. The Doctor arrives after a harrowing trip to Metebelis 3, and when he and the Brigadier have gone, Stevens tells a colleague called Ralph Fell (John Rolfe) that no-one is to descend into the mine. A disembodied voice (John Dearth), identified by Stevens as that of their Boss, tells Stevens to 'process' Fell. 

A miner, Dai Evans (Mostyn Evans), decides to investigate the mine, helped by Dave Davis (Talfryn Thomas) and Bert (Roy Evans) who operate the lift equipment at ground level. He shortly calls for help as his hand is glowing green. Jo arrives and descends into the mine with Bert. The Brigadier and the Doctor are too late to stop them and find that the lift has been sabotaged and the brake does not work. They manage to halt the cage some twenty feet from the bottom of the shaft. In order to get down into the shaft themselves, they need to cut the cable and so they approach Global Chemicals for some cutting equipment. Fell claims they have no such equipment, an assertion contested by Mark Elgin (Tony Adams), another manager at the plant. 

The Brigadier and Dave go off to obtain some equipment - which they eventually appropriate from a nearby garage -and, when the cable has been cut, the Doctor and Dave follow Jo and Bert. 

Meanwhile, Jo and Bert have decided to try and find another way out. They come across a flow of slime down a wall, and when Bert touches it, it burns his fingers and makes them glow green. As his condition worsens, Jo goes on alone and comes to a large pool of slime in which can be seen hundreds of giant white maggots. 

The Doctor and Dave find Bert, and Dave takes him back to the surface. The Doctor goes on and finds Jo. They become trapped when the roof falls in and use an abandoned mine cart to cross the pool of maggots. They make their way up a shaft which emerges in Global Chemicals' factory. On their way up the shaft, the Doctor finds a giant egg which he takes with him. 

They emerge in a room where Fell is supervising the flushing of waste into the mine. Elgin helps the Doctor and Jo escape from the pipe while Fell leaves to report to Stevens. The Boss suggests that Fell be programmed to self destruct. Stevens complies and Fell leaves the office and jumps from a window to his death. 

Back at the Nuthutch, the Doctor and Jo recover from their ordeal, enjoying a meal of cooked fungus courtesy of Nancy (Mitzi McKenzie), who acts as 'Mum' to those at the community. It is clear that Jo and Cliff are getting on very well indeed, much to the Doctor's chagrin. 

Hinks (Ben Howard) tells Stevens about the egg that the Doctor found in the shaft and Stevens orders that it be retrieved. Jo is reading as the egg hatches a maggot which approaches her across the floor. Hinks enters and the maggot attacks him before escaping. 

The Brigadier summons UNIT troops to the area to bomb the mine workings and seal them. The Doctor goes to try and talk to Stevens but he won't listen. He has a visitor from the Ministry - Captain Yates (Richard Franklin). 

With the mine shafts sealed, the maggots emerge via other routes: the shaft leading to Global Chemicals and the slag heaps surrounding the colliery. Bullets have no effect and the Doctor realises a biological deterrent weapon is needed. The Doctor wants to get some oil waste from the factory and so poses as a milkman and a cleaning lady to get inside. Once in, Yates tells him about a special lift to the top floor. 

After accidentally spilling some fungus powder on his microscope slides, Jo decides to get a maggot for Cliff's experiments and heads for the slag heaps. When she has gone, Cliff realises that the powder neutralises the green infection. The Brigadier calls for an RAF strike on the area to try and kill the maggots. Cliff arrives, looking for Jo, and eventually finds her. They head for an old mine entrance to hide while the RAF attack, but the Professor is caught in an explosion and knocked unconscious. 

The Doctor gets into the upper floor of the factory and finds that it contains a massive computer calling itself BOSS - Bimorphic Organisational Systems Supervisor - which is linked to Stevens' brain and which is totally self sufficient. The Doctor is trapped by Stevens and BOSS tries to brainwash him. This doesn't work, however, and he is locked up. Yates releases him but while the Doctor manages to escape, Yates does not. 

The Doctor and Benton rescue Jo and the Professor from the slag heap. Back at the Nuthutch, the Professor is revealed to have a glowing green stain on his neck. He mutters about serendipity, but no-one knows what he means. In Jones' lab, Yates arrives and pulls a gun on the Doctor - he has been taken over by BOSS. The Doctor uses a blue crystal he obtained from Metebelis 3 to free Mike's mind. Mike agrees to return to Global Chemicals to find out more. 

Stevens talks to a Mr James (Roy Skelton), who has been programmed to obey. Yates arrives and, when Stevens leaves him with James, uses the blue crystal to free James from conditioning. James blurts out that the take-over is at four pm before Stevens returns and kills him. 

The Doctor is trying to find the antidote and Nancy brings some sandwiches, leaving the cooked fungus by the window. She then finds a dead maggot by the fungus; it has been killed by eating it. Benton (John Levene) and the Doctor distribute the fungus from Bessie and kill off the maggots. One has pupated into a giant fly which attacks the car until the Doctor uses his cloak to bring the creature out of the sky. 

When the Doctor explains to Jo that serendipity means a lucky accident; she recalls that she spilt fungus on Cliff's slides. Realising that the fungus is the cure to the sickness as well, the Doctor leaves Nancy and Jo to look after Cliff while he returns to Global Chemicals. BOSS and Stevens start their plan to take over the world, and the Doctor gets into the factory. He uses the blue crystal on Stevens, who is freed from BOSS' influence and activates a self destruct sequence. The Doctor runs from the factory as it explodes. 

Cliff recovers and the Doctor finds that Jo wants to go with the Professor on a trip up the Amazon rather than return to UNIT with him. He gives her his blessing. Cliff then asks Jo to marry him and she agrees. The Doctor is saddened, but wishes her well and gives her the blue crystal as a wedding present. As a celebration party starts up, the Doctor leaves on his own in Bessie.

_{Synopsis from Doctor Who: The Third Doctor Handbook by David J. Howe, Mark Stammers and Stephen James Walker, reprinted with permission; further reproduction is not permitted. Available from Telos}