After nearly two thousand years of research and construction, the Morestran Orthodox Church should be almost ready to activate their Energy Tower -- but instead of celebrating their achievement they have cut off all communication with the Omega System where the Tower is being built. A renegade branch of the Cult of Scientists, believing that the Tower is a false means of gaining power for the Church, sends a covert mission to find the fabled Zeta Minor and relaunch Professor Sorenson's original scheme to mine anti-matter. But the mission is infiltrated by a Church secret agent, who transmits the co-ordinates of Zeta Minor back to the homeworld, kills the rest of the team -- and is then killed himself by the creatures which haunt the Planet of Evil.

The Church's greatest agent, Kristyan Fall, was imprisoned for life after betraying them in a quest for personal power; but now they need him again, and he is released and put in charge of the "Zeta Project". Ferdinand du Vindice, a zealot who has devoted his life to destroying the Church, discovers the conspiracy to release Fall, and comes to believe that this is related to the problems with the Energy Tower and the mysterious suicide of Brother Robeson, a brilliant student from the Sorenson Academy. Ferdinand is employed by Hippolito and Antonio, the two brothers who rule the Morestran Imperial families; the Church has promised to share power with the Imperial families once the Tower is complete, but the brothers don't believe this promise will be kept. One of their other agents, who had infiltrated the Cult of Scientists, has joined a mission to discover what's going on at the Energy Tower.

The Doctor, suffering from horrific visions, comes to believe that something is trying to contact him -- something so alien that his mind is destroying itself trying to interpret the messages. He manages to materialize on board the Energy Tower before collapsing into a dead faint, and Tegan and Nyssa set off for help in different directions. Tegan runs into a patrol of Church guards on a mission to seal off part of the Tower -- possibly to entrap the Scientists' infiltration team, or possibly to seal off something far more dangerous. When Tegan claims to have arrived with the Doctor in the TARDIS, she is sent to Kristyan Fall for interrogation. After the events on Zeta Minor passed into legend the Doctor became a holy figure in Church scripture; the Energy Tower itself is designed to tap the kinetic energy of planetary motion just as he'd originally suggested to Sorenson.

The Doctor blocks off his subconscious mind, temporarily saving himself from a nervous breakdown, and sets off to find his companions. He and Nyssa meet Petya, the Imperial brothers' agent and the sole survivor of the infiltration team. The Doctor learns to his horror that the Energy Tower is fueled by anti-matter; somehow the Morestrans have found a way to remove it from Zeta Minor, and the consequences could be catastrophic for both Universes. Just as the rescue ship arrives to collect the infiltration team, they are attacked by an army of anti-men, and Petya gives his life so the Doctor and Nyssa can escape.

The Doctor and Nyssa are smuggled onto a ship returning to Alpha Major, to take their story to the Imperial brothers. On the way they are reunited with Tegan, who seems somehow to have escaped from Fall, and the Doctor delves into his subconscious and manages to communicate with the anti-Universe beings, promising to heal the breach. Ferdinand collects them at the spaceport and takes them to report -- and Tegan, obeying a post-hypnotic command implanted by Fall, tries to assassinate Hippolito. The Doctor stops her, but Hippolito takes advantage of the incident to declare martial law and cut off ties with the Church. As the Morestran Empire prepares for civil war, the Doctor breaks Tegan's conditioning and learns that she overheard a discussion which implies Fall's involvement in something called the "Zeta Project".

Ferdinand is convinced that Brother Robeson's "suicide" was no suicide at all, and the Doctor allows Nyssa to infiltrate the Sorenson Academy and try to learn what she can about the matter. She discovers that Robeson had been murdered upon learning that, due to a fatal flaw in the dimensional equations, the Energy Tower -- source of all the power of the Church and the dreams of the Morestran Empire -- is doomed to failure. Nyssa is contacted by a renegade student, one of the Cult of Scientists, who has learned that other students are vanishing to work on the Zeta Project and intends to sneak on board a mission to "Zeta Major" to find out what's really going on. Nyssa tries to get word to the Doctor, but the Dean of the Academy, upset because she rejected his advances, sends for confirmation of her credentials, learns that she's an impostor, and has her sent to Zeta Major as a project specimen.

The Church officials discover too late that Fall has infiltrated people he trusts into the Zeta Project, and when they attempt to confront him, his associates stage a coup and seize control of the Project. Fall intends to control of the Energy Tower and thus rule the Empire, but first he needs the Doctor's help to stabilise the anti-matter which is already aboard. To this end, he contacts the Imperial brothers and uses video recordings of the original Zeta Minor incident to prove that the blond Doctor they know is nothing like the curly-haired Doctor of legend; convinced that he's an impostor, the brothers agree to turn the Doctor over to Fall. The Doctor realizes that he's being led into a trap and contacts Church officials in order to save Tegan from having to meet Fall again. Tegan and Ferdinand are forced to flee and ally themselves with the Church after Ferdinand shoots Hippolito to save the Doctor's life. The Doctor departs with Fall, hoping to stop the Zeta Project, while Fall refuses to believe the Doctor's claim that it's impossible to stabilise anti-matter. Meanwhile, Antonio takes advantage of his brother's death to declare open war on the Church.

The Doctor has by now worked out what is happening; prisoners were taken to Zeta Minor and exposed to anti-matter, and once they had mutated into anti-men and begun producing anti-matter in their own bodies, they were left on Zeta Minor to maintain the balance while the "surplus" -- the original anti-matter -- was removed from the planet. Zeta Major is an asteroid where the project is continuing -- thousands of peasants and political prisoners are being transformed into anti-men and shipped to Zeta Minor, where an equivalent amount of anti-matter is then mined and removed. Nobody listens to the Doctor's warnings that the interaction of physical laws from two alien Universes will destroy them both...

Ferdinand and Tegan discover the truth about the Zeta Project, and lead a Church taskforce to Zeta Major to destroy it and break Fall's hold on the project. The scheduled shuttle to Zeta Minor is delayed while the pilot waits for the Church ship to leave the vicinity, and as a result the anti-men grow too powerful to control and break free of their bonds. Nyssa, who is herself succumbing to anti-matter contamination, is able to deactivate Major's cloaking sheild in the confusion. Ferdinand locks onto its location and destroys the asteroid with cobalt missiles, but the shuttle manages to disembark -- although its crew is slaughtered by rampaging anti-men. At Tegan's insistence, Ferdinand docks with the shuttle, and the sole survivor -- Nyssa -- is brought aboard their ship, where she succumbs to the anti-matter infection and must be chained up.

Fall takes the Doctor back to the Energy Tower, where they find anti-men roaming the corridors while the physical laws of the other Universe begin to assert themselves. Fall finally realizes that the Project is doomed; he is beginning to succumb to anti-matter infection himself, but he is able to resist it for a time and helps the Doctor to get back to the TARDIS. The Doctor takes Fall to Zeta Minor, where Ferdinand has just destroyed the mining operations -- and attracted the attention of an army of thousands of anti-men. Ferdinand gives his life holding them off while the Doctor pulls the anti-Nyssa into the Black Pool that separates the two Universes. The anti-Universe beings cure Nyssa in exchange for her knowledge of Brother Robeson's discoveries, and send a representative to destroy the anti-men on the surface of Zeta Minor.

The Doctor takes the survivors back to the Energy Tower, where they discover that the Imperial and Church fleets have fought each other to mutual destruction over control of the doomed Tower. The survivors flee in escape pods, while the Doctor and Nyssa activate the Tower and open the dimensional rifts. As Robeson had proved, the rifts are unstable, but the anti-Universe beings are able to use them to emerge and absorb the Tower into the structure of their being, becoming whole again at last. Realizing that he will never be cured of his condition, Fall flees into the corridors of the Tower and is killed by the enroaching anti-Universe beings. The Doctor, Nyssa and Tegan escape in the TARDIS as the rifts close, leaving the scattered remains of the Morestran Empire to pull themselves together and try to make a fresh start.