For me it has to be the terminal of Keys being turned into the proto-Gravemind (Halo Anniversary - Terminal 9: Keyes (Audio Fix) - YouTube)
Him pleading with the gravemind to not erase his memory of Miranda Keys always gets me right in the damn feels
Hey OP, we already have a very similar topic that’s still active / open:
https://www.halowaypoint.com/en-us/forums/f9237adeaf1742c09de144d7bf3f7507/topics/what-was-your-most-emotional-moment-in-halo/5a354f34-2fd4-4485-9e83-ddd0fbde0a31/posts