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The TARDIS zoo was, as the name suggested, a zoo in the Doctor's TARDIS.
History
Most of the animals in the TARDIS zoo were endangered, and the the Doctor hoped to relocate them to suitable habitats. They were kept in synthetic habitats that were small cuboid boxes. The Sixth Doctor brought a Kymbra Chimera into the zoo while it was disguised as a Swuffle. It broke free and caused a small amount of damage that resulted in several other creatures escaping. (DWM: Changes)
Ace discovered the TARDIS zoo while exploring the ship. She let out a dodo, but it bit her and fled. She caught it and returned it to the zoo. (ST: Echo)
The Tenth Doctor kept another dodo in the zoo. (NSA: The Last Dodo)