Petty Officer 2nd Class Cuyler Burnett Condon and Seaman Dimitri Isacc Morales died in separate incidents following the ship's arrival.
Capt. Zaldy Valenzuela and Cmdr. Art Palalay were fired from their respective positions on Sunday.
The carrier spent nearly a decade based in Japan before arriving back in the states this week.
The aircraft carrier's departure comes at a time of growing tension in the face of increasingly assertive China in the Indo-Pacific.
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