The Doctor attempts to halt Mestor's true plan for the planet of Jaconda, Azmael has a decision to make for his world.

The Doctor, Peri and Hugo Lang arrive on Jaconda only to discover the massive devastation that the planet has suffered. Azmael is told about the destruction of the Titan 3 outpost.

The Doctor and Perry arrive at the facility on Titan 3 where Romulus and Remus are being held. The Doctor is taken prisoner by one of the Professors guards. When the Doctor is brought to the professor he recognizes him as Azmael the Master of Jaconda.

The twin human children Romulus and Remus are kidnapped by the mysterious professor Edgeworth. The Children appear to be genius's. Meanwhile the Doctor seems to be having stability problems with his new regeneration and is acting erratically.

Chellak and his men attack Jek's base. The Dr. crash-lands the ship, and must escape from his captors to find the antidote to the Spectrox poisoning and save Peri. He does so, but at a staggering cost.

The Doctor escapes the Mag,a creature and is taken prisoner by the gun runners; The real Salateen takes Peri back to General Challek and is then kidnapped again by Sharaz Jek.

Sharez Jek and his androids save the Doctor and Peri from execution when he rescues them. Then he takes a shine to Peri and wants her with him forever. Later the Doctor and Peri find out they are dying from Spectrox Toxemia, having been poisoned when they handled the Spectrox nest upon first entering the cave system.

The Doctor lands on one of the twin planets of Androzani where he along with Peri are mistaken for gun runners and sentenced to death.

In order to complete his plan to bring himself back to full size after his accident with his tissue compression eliminator, The Master tries to destroy the Doctor. Turlough makes a decision and tells the Doctor why he was exiled to Earth.

Turlough is taken to his fathers ship, the Doctor and The Master battle for control of Kamelion so The Master can go through with his plan.

The Master strengthens his control over Kamelion in order to be able to complete his goals and tries to get Peri under his control.

The Tardis receives a distress signal and at the same time Kamelion seems to be having problems while linked into the Tardis. Following the distress signal the Doctor arrives on Lanzarote and Turlough rescues Peri. Turlough seems to know where the distress signal is coming from.

The Daleks capture the Doctor and plan to duplicate him and his companions as part of their plan to attack the high Council of Gallifrey. Davros starts converting Daleks and their helpers over to his control.

The Doctor starts having problems navigating the TARDIS through the space-time vortex and ends up on Earth in the future where strange events are going on with imitation police officers and soldiers from the future.

The Doctor tries to deal with the Tractator's cunning plan, despite Turlough's best intervention. They discover the splintered TARDIS in the tunnels beneath the planet's surface, but how will they put it together again?

Turlough starts to regain ancestral memories of the Tractators, the Doctor having discovered the Tractators works to discover what their plan is.

The Doctor works to help the injured colonist, Tegan discovers a file in a closed drawer called "Deaths Unaccountable". Meanwhile, Plantagenate works to convict the Doctor of being the source of the attacks on Frontios.

In the far distant future, the few remaining survivors of the human race struggle to survive on the planet Frontios. The Doctor states that the Laws of time do not allow him to have contact because the survivors must go their own way without outside intervention at this key point in time.A meteor storm hits the planet and starts to drag the TARDIS down with it, the Doctor is unable to stop the TARDIS from making a emergency landing.

The Malus is forcing the towns people to preform the re-enactment for real as it needs the psychic forces created by the suffering of war to feed off of and recharge it's energies. It is up to the Doctor to prevent the Malus plans from reaching fruition.

The TARDIS arrives in Little Hodcombe, Tegan wants to visit her Grandfather while they are there. Also, a war re-enactment is going on that starts to get more and more out of hand and realistic for unknown reasons.

The Doctor is presented with a moral dilemma when Icthar reveals his plans to get rid of the human race so the Silurians can take back what was once theirs.

While the Silurians and Sea Devils attack the bases air locks, the saboteurs take advantage of the distraction to go ahead with their own plans.

Just as the doctor is starting to gain a tentative trust from the humans of the underwater military base, an unknown cruiser appears and the Doctor seems to recognize it and warns the humans not to fire upon it.

The Doctor materializes the TARDIS inside a underwater military base in 2084 during wartime. The base is about to be attacked on two fronts, secret agents within and a unknown enemy outside of the base.