When jedi master Qui-Gon Jinn was attacked by a Sith warrior, Windu was in disbelief, but he promised to discover the identity of the attacker. It was Mace Windu who tested the young Anakin Skywalker, when he was referred by Qui-Gonn as the "chosen one". Mace Windu and Yoda alerted the young boy about fear and the path to the dark side.

  Windu, also recommended Qui-Gonn to stay focus on his main purpose, which was to protect the queen, at all costs, so he told Qui-Gonn to gave up the training on Anakin for the time being.

  Later, at the funeral pyre of Qui-Gonn, Mace Windu and Yoda discussed about the identity of the attacker of the late Qui-Gonn, knowing for sure that was a Sith warrior. Now the question remained: it was a master or an apprentice?