A superluminal signal is sent to Earth, carrying with it an unusual energy blob that seems intent on capturing the Third Doctor. In the meantime, the homeworld of the Time Lords is under siege, with all the power sustaining it being drained through a black hole. Trapped and desperate, the Time Lords do the unthinkable and break the First Law of Time, allowing the Doctor to aid himself by summoning his two previous incarnations from the past.
Unfortunately, the First Doctor is trapped in a time eddy, unable to fully materialize, and can only communicate via viewscreen, but the Second Doctor joins the Third in investigating the origins of the creature and the black hole, while UNIT headquarters faces an attack by the gel-like alien creatures.
The First Doctor deduces the black hole is a bridge between universes, and the other two Doctors allow the TARDIS to be swallowed up by the energy creature, which transports them, Dr Tyler, Jo Grant, Sergeant Benton and Brigadier Lethbridge-Stewart into an antimatter universe created by the legendary Time Lord Omega. Omega was a solar engineer who created the supernova that powers Time Lord civilization, but was considered killed in the explosion. In actuality, he had been transported to the antimatter universe, where his will and thought turned the formless matter into physicality. Trapped, due to the fact that his will is the only thing maintaining reality, he vowed revenge on the Time Lords who left him stranded.
It is clear that the exile has made Omega quite insane. Along with his revenge, he has summoned the Doctors here to take over the mental maintenance of the antimatter universe so he can escape. However, the Doctors discover that years of exposure to the corrosive effects of the black hole's singularity have destroyed Omega's physical body - he is trapped forever. Driven over the edge by this discovery, Omega now demands that the Doctors share his exile.
The Doctors escape briefly, and offer Omega a proposition. They will give him his freedom if they send the others back to the positive matter universe. Omega agrees, and when that is done, the Doctors offer Omega a force field generator containing the Second Doctor's recorder, which had fallen in it prior to the transport through the black hole. Omega knocks the generator over in a rage and the unconverted positive matter recorder falls out of the force field. When the recorder comes into contact with the antimatter universe, it annihilates everything in a flash, returning the Doctors in the TARDIS to the positive matter universe. The Third Doctor explains that death was the only freedom anyone could offer Omega.
With the power now restored to the Time Lords, they are able to send the First and Second Doctors back to their respective time periods. As a reward, the Time Lords give the Third Doctor a new dematerialization circuit for the TARDIS and restore his knowledge of how to travel through space and time.