The Master, in the guise of Professor Thascales, has constructed at the Newton Institute in Wootton a device known as TOMTIT - Transmission Of Matter Through Interstitial Time - with which to gain control over Kronos, a creature from outside time. The creature is summoned but the effect proves uncontrollable, so the Master flees.

The Doctor shuts TOMTIT down but the Master later reactivates it, using it first to ensnare Krasis, High Priest of the lost city of Atlantis, and then to attack UNIT forces by way of a series of timeslips. The Master takes Krasis back to Atlantis in his TARDIS in the hope of stealing the sacred Crystal of Kronos, with which he aims finally to dominate the creature. The Doctor follows with Jo but is unable to prevent his enemy from seducing Queen Galleia and staging a coup. Galleia turns against the Master when she learns that he has caused the death of her husband, King Dalios.

The Master then unleashes Kronos, destroying Atlantis. The two Time Lords escape in their respective TARDISes and confront each other in the time vortex. The Doctor threatens to trigger a 'time ram' - a devastating collision - but cannot bring himself to do it.

Jo, held hostage by the Master, has no such qualms, and operates the controls herself. The two TARDISes reappear in a strange void presided over by Kronos - who now appears as a beautiful female face.

The time ram has released Kronos, who agrees to return the Doctor and Jo to Earth. The creature plans to subject the Master to eternal torment, but the Doctor pleads on his behalf and he too goes free.