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Tom had inherited a love of birdwatching from his naturalist father, Professor Brian Phipps, so he was able to guide the Doctor on a trip in Bessie into the countryside around Tom's house. During the trip, they encountered what appeared to be a freak tornado. On returning home, they found the Phipps' house had been completely destroyed by the tornado.
The Doctor realised the "tornado" was interested in him specifically, so he decided to distance himself from the Phipps' family and spend the night camping on a remote hill. Unbeknownst to his parents, Tom came to the Doctor's campsite just in time to be sucked up into the returning "tornado". The vortex turned out to be a conduit to an alien space ship in orbit above the Earth. The two swiftly worked out that they had been captured for a menagerie of life-forms, already onboard. Not wishing to remain in a zoo, they worked together to understand the unusual biotechnology of the vessel. They figured out how to "reverse the programming" and get themselves re-deposited on Earth. (COMIC: The Vortex)
Behind the scenes Edit
By the standards of most eras of Doctor Who, Tom wouldn't qualify as a companion. However, for the exile on Earth period, he's quite comparable to Liz Shaw or the early season 8 Jo Grant. He begins the story helping the Doctor on a question of scientific curiosity, then suddenly is whisked into an adventure with Earth invaders.