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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". Space Services were on secret mission to locate the missing Agent. (DWAM: 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) (DWAM: 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. DWAM: The Secret Star Trail
