Aeris in ff rebirth? I'm not really sure what happened cause I didn't play the sequel.
SPOILER for XenobladeCrono in Chrono Trigger.
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Pyra and Mythra in Xenoblade 2.
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That's the one I was going to go with.Commander Shepard. Probably the most obvious Christ allegory in gaming. He's a Shepard who dies, comes back from the dead, and then returns to the heavens to save humanity.