Matrix Rassilon

After his physical death, a version of the mind of Rassilon stayed active in the Matrix, ruling Gallifrey from the shadows as the leader of the Matrix Lords. He manipulated the Doctor into performing many missions for him.

Rule from the shadows
Greatest and oldest of the Matrix Lords, Rassilon oversaw their use of the APC Net to boost their mental powers and continue to influence the outside universe. They also created the Celestial Intervention Agency to act on their behalf in the land of the living. (PROSE: The Legacy of Gallifrey) CIA operatives were often unaware that they were working for Rassilon rather than for the Lord President or some other Time Lord superior. Hence, Rassilon continued to rule Gallifrey, subtly shaping its history as he saw fit, though not all of the Presidents were aware of this.

To keep the balance of the universe, Rassilon created two projections of absolute good and absolute evil and gave them the Key to Time, allowing them to stop the universe and put things right if the balance between chaos and order was upset; (PROSE: The Legacy of Gallifrey) these Guardians of Time were known to the Time Lords and respected by them. (TV: The Ribos Operation)

Within the Matrix, Rassilon also sat as the representative of the Matrix Lords, with other advanced beings who collectively called themselves High Evolutionaries and who had some involvement in the affairs of the universe. The High Evolutionaries sometimes used the Gallifreyan construct known as Shayde on their behalf. (COMIC: The Tides of Time)

Use of living agents
Besides the CIA, Rassilon wished to have a free agent in the outside universe, and decreed that it should be a minor renegade known as the Doctor. Using his influence, Rassilon began manipulating the Doctor's life in his second incarnation, though it was not until he faced the Great Intelligence in the London Underground that he began to suspect he was being used. The CIA eventually contacted him an official basis, and sent him on a mission to prevent the Sontarans from gaining mastery of time travel. In the process, the Second Doctor accidentally broke the First Law of Time (PROSE: The Legacy of Gallifrey) by meeting the Sixth Doctor. (TV: The Two Doctors)

Terrified of the consequences of this transgression, the Doctor continued running, but eventually required the Time Lords' help to put right the machinations of the War Lords. The Doctor was put on trial, but one of those who judged him was Socra, secretly one of Rassilon's CIA agents, who was instructed to keep tabs on the Doctor during his exile on Earth. It was Socra who persuaded the president, Pandad IV, to let a member of the High Council warn the Doctor about. (PROSE: The Legacy of Gallifrey) This Time Lord messenger allowed the Third Doctor to anticipate the Master's attack of Earth with the help of the Nestene Consciousness. (TV: Terror of the Autons)

The Matrix Lords had been unable to predict Omega's return because he was trapped in an anti-matter universe, thus inimical to Gallifrey's very nature. (PROSE: The Legacy of Gallifrey) After the Doctor proved instrumental in ending the threat of Omega, (TV: The Three Doctors) Rassilon authorised Socra to reveal the CIA's existence to President Pandad IV, and make it public, if it was necessary to convince the President to free the Doctor from his exile. However, while the Doctor's exile was lifted, Pandad IV declined the offer to go public, feeling that widespread knowledge of the CIA would risk lessening the population's faith in the Presidency. (PROSE: The Legacy of Gallifrey)

Chancellor Borusa, who had known the secrets of the Great Key and the Sash, (TV: The Deadly Assassin) eventually became Lord President of the High Council. This outraged Rassilon, as it broke the regulations he had put in place to avoid all powers being concentrated in any other individual but himself. Claiming to his fellow Matrix Lords that he foresaw a time when Borusa's presidency would lead Gallifrey to destruction, (PROSE: The Legacy of Gallifrey) even though his government had succeeded in saving Gallifrey from Omega a second time, (TV: Arc of Infinity) Rassilon reactivated the Death Zone for the first time since his physical death, and beguiled Borusa with the promise of immortality to be dispensed in the Dark Tower.

Borusa first sent two of his own High Council into the Death Zone, Thalia and Zorac, but they were struck down by bursts of psychic energy converted into elemental weaponry that resembled lightning bolts, fired by Rassilon himself from the astral plane of the Matrix. After Borusa finalised his scheme by sending the five first incarnations of the Doctor to serve as his scouts, (PROSE: The Legacy of Gallifrey) he confronted a projection of Rassilon hovering above Rassilon's ancient body, who cursed him with the immortality of a living statue in punishment for his hubris. The Doctors were returned to their travels, (TV: The Five Doctors) and, with Rassilon's blessing, Flavia became the new President of the High Council, returning to the old traditions by obtaining an intelligent cat to act as her advisor, whom she decided to name "Doctor". (PROSE: The Legacy of Gallifrey) Rassilon also granted the First Doctor the ability to pilot the TARDIS effectively in gratitude for stopping Borusa, allowing tie up some of the loose ends he had left while he was approaching his first regeneration. (PROSE: The Witch Hunters)

The final loose end tied up by Rassilon was to allow to escape Gallifrey unscathed, an act which was recorded by the Celestial Intervention Agency, although they were mystified by it. (PROSE: CIA File Extracts)

Meddling with the Doctor's timeline
After President Romana reconciled Gallifrey with the Sisterhood of Karn, lifting the Curse of Pythia, (PROSE: Lungbarrow) the Book of Lies said that, from within his tomb, the "Great Grey Eminence" made a deal with Faction Paradox to fold the Doctor's timeline back on itself and return Gallifreyan history to passionless sterility. (PROSE: Unnatural History)

When 's last trap left the Eighth Doctor suffering from amnesia, Rassilon's spirit guided the Doctor to various locations where his past selves were about to face crucial dangers or defining moments. In the process, the Doctor made "improvements to the pattern of history" for Rassilon. At the end, Rassilon guided the Doctor to Sam Jones, (PROSE: The Eight Doctors) who he knew would never dare to "screw" the Doctor. After Gallifreyan history was rewritten, (PROSE: Unnatural History) Flavia was the current President, (PROSE: The Eight Doctors) and the "Eminence" had been taught the ways of paradox. However, these changes to Gallifrey's history were unstable, and the Doctor wasn't sure if Flavia or Romana was President, (PROSE: Unnatural History) or if he had parents or been born of a Loom. (PROSE: The Shadows of Avalon)

Rassilon and the other Evolutionaries once hired the Threshold to stop a Dalek attempt to invade other realities. (COMIC: Fire and Brimstone) They sent Shayde to help the Eighth Doctor destroy the Threshold base at Wormwood located on Earth's Moon. (COMIC: The Final Chapter)

In the Divergent Universe
From within the Matrix, Rassilon began to manipulate the Eighth Doctor into destroying the Divergence, arranging for him to be possessed by the essence of anti-time and appearing to him before this happened as well as saving him, so that he could become the destructive Zagreus and be used against Gallifrey's enemies. Rassilon possessed the body of Leela – the only body on Gallifrey that he could influence without setting off mental alarms – and used Romana II to teleport them past the barriers in the Death Zone which was her presidential right. He did this to obtain the Ring of Rassilon and unlock his Foundry. He then tried to force Romana to resign in favour of Zagreus, believing that this would ensure the destruction of the Divergence. Rassilon formed an alliance with the Doctor's TARDIS, which had also been infected with anti-time, promising to release its consciousness from the infection while using its body to create a sword of anti-time, with which he hoped Zagreus would kill the Divergence.

However, his plan failed when the Doctor refused to kill, proclaiming his status as the Doctor. Rassilon then used the anti-time sword to kill Matthew Townsend, Tepesh, and Walton Winkle, who had seen the Divergence and been re-constituted in the Matrix with parts of the Doctor. Although Rassilon had hoped that the deaths of his other selves would further break the Doctor, this failed when, at the Doctor's behest, Charley Pollard used the anti-time blade on him. However, he gave into his Zagreus persona to survive with the help of the aspects of himself released when the three were killed, recognising that Rassilon was the real threat. Armed with the anti-time blade, Zagreus refused to be Rassilon's puppet and cast him into the Divergent Universe to end his actions. (AUDIO: Neverland, Zagreus)

Indeed, at some point prior to being cast into the Divergent Universe, Rassilon had regained a physical form outside of the Matrix, allowing for his survival. Now trapped in a new universe, Rassilon planned to steal the Doctor's TARDIS and escape, using the Kro'ka as his puppet. The Doctor eventually thwarted Rassilon's plans, however, and left him behind. Rassilon's temporal senses broke down as the universe's time-looped nature left both himself and the Kro'ka trapped in a repeating pattern, while the Doctor and his companions returned to the main universe. (AUDIO: The Next Life)