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Baltra was created along with all other Matoran to work inside the body of the Mata Nui robot to keep it functioning. When he began to have problems with his ability to work properly, he, along with his "brother" Balta, was sent to Karzahni to be repaired. However, he was weakened during the rebuilding process, and was sent to live on the Southern Continent.
During the Great Cataclysm, the area on the Continent where Balta and Baltra lived broke through to the surface of Aqua Magna, becoming the island of Voya Nui. He worked in the Voya Nui volcanic lab for most of the rest thousand years, and he was quite content with his job.
When the Piraka came to Voya Nui, he managed to escape from them, and attempted to get help from the Toa of Metru Nui. He somehow made his way back to the Matoran Universe beneath Voya Nui, but was captured by a Makuta, who used him as part of an experiment, and was mutated into a Toa-like form.
He later woke up as a Toa-like warrior. He escaped from the Makuta's lab, but when the Makuta noticed that his experiment was gone, he pursued Baltra until he caught the Toa, and managed to use a Shadow Leech on him. However, Baltra was saved from being completely turned to Shadow when a small Rahi ate the Leech. Baltra escaped again, now possessing some Shadow powers as well, and was determined to take revenge on the Makuta that had imprisoned him.