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Musa was abducted with his fellow candidates in 2517. His body rejected the augumentations, forcing him to use a wheelchair for the rest of his life. He felt a grudge against Catherine Halsey and the Office of Naval Intelligence for allowing Dr. Halsey to experiment on, and eventually kill some of the candidates. Musa found that while the SPARTAN-II Program was immoral, it was important, and with the forces of the Spartan-II's largely depleted, and the threat of Insurrection and Covenant remnants due to rise, he concluded that humanity needed more Spartans to be created. In January 2553 he and several Admirals met at HIGHCOM Facility Bravo-6 and discussed the details of the proposition of the SPARTAN-IV program.
With Jun-A266's aid, Musa selected five soldiers, Sarah Palmer, Edward Davis, Yeong-Hao Holst, Vladimir Scruggs and Joel Thomas, to be the newest generation of Spartans. After the Spartan-IVs received their augmentations, they put them in a training exercise without armor against regular marines, the objective being to get to the trigger button. However, everyone but Palmer had been quickly eliminated before the exercise was over. Scruggs complained that they should get their armor, but Musa appeared to tell everyone that they have to earn it first. He lectures the Spartan-IVs, telling them the importance of teamwork, not grabbing glory for oneself. He then sent them to UNSC Infinity, where they fortuitously foiled the New Colonial Alliance faction of the Insurrectionists from stealing the ship.
Musa later met with HIGHCOM, criticizing them for turning Ilsa Zane, an original Spartan-IV rendered unstable by her enhancements, into a monster, further more that ONI were deluded to think they could control her. He then discusses the successes of his Spartans, before declaring that the Spartans will operate independent of the Navy or ONI.