The Logopolitans quickly drag the shrinking TARDIS back to the center. They are watched by the Master.
Knowing there is a fault in the calculations, the Monitor and Adric begin to check the registers for mathematical errors. As they search, the Monitor explains that people have to do the block transfer computations, as the calculations themselves would affect computers. They continue their investigation into the streets.
The Logopolitans use sonic projectors to create a stasis zone around the TARDIS to keep it from shrinking futher.
The Monitor and Adric find the source of the error – several Logopolitans murdered and shrunk by the Master. The Monitor laments that sabotaging Logopolis is the most dangerous crime in the Universe.
They write down the corrections and Tegan holds the paper in front of the TARDIS so that the Doctor can make repairs.
Adric and Nyssa go to look for the mysterious Watcher, who Adric believes to be the Master. Nyssa is approached by the Master, who pretends to be her father. He explains that he intends to discover the secret of Logopolis and puts a golden bracelet on her wrist.
The TARDIS swells back to its normal size and the Doctor emerges. He tells Tegan of her aunt's death, then retrieves Adric and Nyssa from the streets.
The Master kills two more Logopolitans and steals the sonic projectors. He then uses them to silence the Logopolitan calculations. The Monitor pleads with him to stop as he is releasing entropy. The Doctor returns and tells the Master he is destroying Logopolis.
Adric tries to move the sonic projectors but the Master uses the bracelet to make Nyssa strangle him until Tegan replaces them.
The Doctor again pleads with the Master to stop but the Master is unmoved. He switches off the sonic projector but the silence remains. They find the buildings collapsing into dust and the Logopolitans dead. The Master tries to use Nyssa against the Monitor, but the bracelet breaks.
The Monitor tells them entropy is now spreading out of control and will unravel the structure of the Universe. The Universe long ago passed the point of heat death but the Logopolitans kept it open by using the antenna to create voids into other universes. Now that Logopolis is dead, the Universe will decay.
As the planet decays, the Doctor proposes an alliance with the Master to save the Universe. The TARDIS materializes nearby and the Doctor sends his companions in. He then take the Master's hand…