Numerous times III through Lodi calls Ikora “Commander.” They even make a point to stress this in the final cutscene with a dramatic pause.
Ikora is not a Commander…. Zavala is.
RIP
The Old Vanguard.
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Zavala isn’t a guardian anymore so he’s likely not the Vanguard commander now. Although it was a bit jarring to hear this, that’s likely the reason.