The story made up of episodes 13-14 is generally referred to as The Ultimate Foe.

The Inquisitor calls the Keeper of the Matrix (James Bree) into the Court and he denies that the Matrix can be tampered with as the Doctor has alleged. He states that entry into the Matrix can be achieved only with the Key of Rassilon, which he alone holds. The Doctor accuses the Valeyard of tampering. 

Two coffin-like containers arrive at the trial ship. Inside the pods are Glitz and Mel, who enter the courtroom. Glitz states that he has been sent here to assist, and when the Inquisitor asks by whom, the reply comes from the Matrix screen. An image of the Master appears, proof that the Matrix can indeed be breached - the Master has a copy of the Key of Rassilon. 

The Master wants Glitz to testify, so the Doctor asks him about the secrets. Glitz reveals that the Sleepers from Andromeda had been stealing secrets from the Matrix while based on Earth. The Master confirms this and goes on to explain that the High Council of Time Lords used a magnetron to throw Earth across space, causing the fireball which devastated it. They then arranged for the planet to be renamed Ravolox, so as to divert suspicion from themselves. Fearing that the Doctor would discover the truth, the Council made a deal with the Valeyard to the effect that he would receive the Doctor's remaining regenerations upon the Doctor's execution. The Master also reveals that the Valeyard is an amalgamation of the Doctor's darker side, somewhere between his twelfth and final incarnation. 

The Valeyard flees into the Matrix through the Seventh Door, which is located just outside the courtroom. The Doctor follows, taking Glitz with him, and finds himself in a fantasy world created by the Valeyard. After many deceptions, he confronts his future self, who had disguised himself as a Dickensian clerk named Popplewick. 

The Doctor realises that the Valeyard intends to wipe out all the Time Lords present at the trial by using a device - variously described as a megabyte modem, a maser and a particle disseminator - which he has secreted in the Matrix and which is linked to the screen in the courtroom. The Master, meanwhile, intends to use the ensuing chaos on Gallifrey to take over as the supreme ruler of his own people. He has enlisted the services of Glitz, but his plans are halted when he becomes trapped inside his TARDIS in the Matrix. 

The Doctor induces an anti-phase signal in the telemetry unit, causing the particle disseminator to backfire. Mel, who had followed him into the Matrix, has already gone back to warn the Time Lords in the court, and they escape unscathed when the machine blasts energy through the Matrix screen. The Valeyard is apparently killed in the back-blast. 

The danger over, the Doctor returns to the courtroom, where the Inquisitor informs him that all charges against him have now been dropped. She is also able to tell him that, contrary to what was seen in the trial evidence, Peri was not killed on Thoros-Beta but is now Yrcanos's Queen. 

As the Doctor prepares to leave, the Inquisitor invites him to run once again for President of Gallifrey. He declines, asking only that the new Council treat the entrapped Glitz with clemency. He then departs with Mel in the TARDIS. 

As the Inquisitor leaves the court she asks the Keeper of the Matrix to arrange all necessary repairs. When the Keeper turns, however, he is revealed to be the Valeyard.

Synopsis from Doctor Who: The Sixth Doctor Handbook by David J. Howe, Mark Stammers and Stephen James Walker, reprinted with permission; further reproduction is not permitted. Available from Telos