Until Disco S3, “Living witness” was the furthest future we had seen in Star Trek. But Academy takes place after Discovery. At the end of “Living Witness” the Doctor is described as heading towards Earth.
Assuming the burn didn’t get them, it’s entirely possible two EMHs are surviving in Discovery’s time. I think it would be a fun twist if it wasn’t the EMH we expect!
Only reason I think they might not go this route is that it could make it hard for them to drop in Prodigy references. Although, they could definitely have the two EMHs talking to each other…
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