Agent 99
Agent 99 first came to the Doctor's attention when he was listed in a classified file found on board a crashed space freighter on Thosis, otherwise known as "The Moon of Lost Hope". The Space Service crew were on secret mission to locate the missing Agent. (DWA: The Moon of Lost Hope)
Agent 99 was somehow believed to be involved in the defeat of the Koth-Kulaar who was believed to be condemned to a dimension-warp back in the Bad Old Days.
A later encounter with the peaceful Xragoni gives the Doctor the last known location for Agent 99 (unbeknown to another Space Services team searching for the Agent) (DWA: The Deadly Mutant)
The Doctor's curiousity led him to track down the missing Agent ("the greatest secret agent in Earth's future") using a telepathic signature he obtained from a hypernet station which he later used with the powerful thought crystals of Lossk to locate him on the planet Quiox.
Agent 99 had been living a peaceful life among the savage wildlife that included the giant Night Butterflies who regarded Agent 99 as their leader. Agent 99 rescued the Doctor from the butterfly larvae and having reconsidered his position decided it was time to return to his neglected duties on Earth accepting a lift in the TARDIS. (DWA: The Secret Star Trail)
As soon as Agent 99 arrived, there was an attempt led by Inspector Gleave to arrest him - an attempt that was thwarted by their escape. But when the Doctor's travelling companions (Amy Pond and Rory Williams) are captured, Agent 99 and the Doctor give themselves up to the council who reveal that Agent 99 (the last Warp Agent) had concealed in his tatooed chest, a live dimension warp which was activated to release the Koth-Kulaar from its long exile and captivity. (DWA: Agent 99)
Saved by the Koth-Kulaar's short reign of destruction on Earth Agent 99 already in a weakened state offered to use his last remaining strength to link up to the TARDIS systems and use his dimension warp one last time to send the Koth-Kulaar back into oblivion. Once the threat had been removed the Doctor used the TARDIS to take them into a remote area of space where Agent 99's body was allowed to float freely among the stars with the universe safe for as long as his body remained offline. (DWA: Dimension Warp)