The Doctor and Jo

After working all night in his lab on a device to help UNIT locate The Master, The Doctor experiences a dream in which he sees a trident-shaped crystal and his arch enemy. On waking, Jo Grant mentions Atlantis and The Doctor's interest is piqued. He summons The Brigadier, who is not interested as he is due to attend a demonstration of a device called TOMTIT – ‘Transmission Of Matter Through Interstitial Time’ - at the Newton Institute in Wootton just outside Cambridge.

The man behind TOMTIT is The Master, posing as Professor Thascales. He hypnotises Doctor Charles Percival at the Institute when he becomes suspicious. At the heart of TOMTIT is the trident-shaped crystal. With The Master gone, his assistants, Doctor Ruth Ingram and Stuart Hyde, decide to run a test before the demonstration. However, when Ruth and Stuart start their test a time sensor that The Doctor has built, which detects disturbances in the time field, starts to register allowing The Doctor to identify the rough location of the disturbance.

The Master, on learning that UNIT personnel will be at the demonstration, disguises himself in a radiation suit. The Doctor picks up the signal, enabling him to indentify its exact source, which prompts him to rush to the Institute. At the climax of the demonstration, The Master shouts out a summons to Kronos and then hurries out just as The Doctor and Jo arrive, but Jo is caught in a time field and frozen. The Doctor gets Ruth to reverse the temporal polarity and the machine stabilises. Stuart, however, has aged into an old man. The Doctor realises that Thascales is The Master and Stuart raves about the crystal and seeing Kronos. The Doctor goes with Ruth to check the crystal and recognises it as the Crystal of Kronos - The Master is trying to capture Kronos a Chronovore. The Doctor powers the machine up and Sergeant Benton is unable to move the crystal. This is because it isn't really there at all. It is linked to or is the same as the crystal in Atlantis.

The Doctor and Jo

The Master knocks Sergeant Benton out and activates TOMTIT. This causes Krasis, a High Priest in Atlantis, to be transported to the Institute. Sergeant Benton manages to escape and warns The Doctor. The Master uses a medallion from Krasis to enter the equations to summon Kronos. Kronos appears as a giant white bird-like creature and Stuart returns to normal as time feeds back. The Master though cannot control the Chronovore and returns Kronos to the crystal after it had devoured Percival. Krasis tells The Master that this crystal is only a fragment of the true crystal which is still in Atlantis and guarded by a Minotaur.

The Master drains the energy from the crystal so he can take it to Atlantis. UNIT troops headed by Captain Mike Yates, are on their way, called for by The Brigadier, and The Master summons a knight in armour, Roundheads and a World War II flying bomb to try and stop them. The Doctor travels out to meet them as they are also bringing the TARDIS. To try to stop The Master from leaving, The Doctor moves his TARDIS inside The Master's TARDIS. However The Master's TARDIS also ends up inside The Doctor's TARDIS. The Master then activates TOMTIT and enters his TARDIS. However, The Doctor is unable to make The Master listen to him over the TARDIS' communication system and so leaves his TARDIS to confront The Master directly. The Master summons Kronos to devour The Doctor and then separates the TARDISes in the vortex, sending Jo in The Doctor's TARDIS spinning away.

The Master as Professor Thascalos

The Doctor manages to contact Jo through the TARDIS' telepathic circuits and she is able to bring him back unharmed. Back at the lab, The Brigadier and his UNIT troops are frozen in time and Ruth and Stuart try to reverse the effects of the machine but manage instead to transform Sergeant Benton into a baby.

When The Master arrives in Atlantis he starts making plans to obtain the crystal but King Dalios does not respond to him so he decides to seduce Queen Galleia instead. When The Doctor and Jo arrive, Dalios is sympathetic. Jo follows Hippias and Krasis but finds herself thrown into the labyrinth where she confronts the Minotaur. Galleia's handmaiden, Lakis, alerts The Doctor and Dalios and The Doctor manages to defeat the Minotaur but not before the Minotaur kills Hippias. Returning to the palace, The Doctor and Jo find that The Master is now King. He has The Doctor and Jo thrown in to a dungeon where they are shortly joined by Dalios who, before he dies, tells The Doctor he must save the world.

Queen Galleia introduces The Master as King but is unaware that Dalios is dead until The Doctor reveals this. Krasis operates the TOMTIT device and summons Kronos who starts to destroy the city. The Master takes the crystal and heads for his TARDIS but Jo leaps on him and is carried along as he leaves. The Doctor makes chase in his own TARDIS. He intends to ram The Master's ship but cannot bring himself to do it as he knows that this action will result in the death of Jo. Jo though makes the decision for him and operates the appropriate controls in The Master's TARDIS.

Doctor Ruth Ingram and Stuart Hyde

This results in The Doctor and Jo finding themselves in a featureless void where they come face-to-face with Kronos who now looks and sounds like a woman. She is grateful to The Doctor as he has released her and offers to grant his desires. All The Doctor and Jo want is to return home. She intends to punish The Master. However, when he pleads for his life, The Doctor intercedes and asks that he go free so that he can be returned to the authorities on Earth. Kronos agrees. The Master though seizes the opportunity and escapes in his own TARDIS.

Back at the Institute Ruth finally manages to reverse the time field and The Brigadier and the UNIT troops are freed. The machine then explodes and Sergeant Benton is returned to his normal age, standing naked in the laboratory, completely oblivious as to what has been happening.