By A Mystery Man Writer
In Cell's original timeline, an alternate Future Trunks went into the past and helped Goku just as in the main timeline. Future Trunks and the Z Fighters manage to defeat the Androids and he travels back to his alternate future timeline. Since this was a completely different timeline, the events of Cell never occurred and he did not expect to encounter Cell (and may not have even been aware of Cell's existence). When he returned to Age 788 of his alternate future timeline, he disabled the other
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