There's two unused doors, they got blocked off. So I put did some quick level editing to renable them. One of them turned out to be a door to the hanger bay missing from the trailer, oddly enough it looked like an important place as you get locked off by a super missile door. The other unused door seems to be a debug short cut to the Omega Metroid fight. IDK if the regular door at the bottom just gets replaced with this door or if it's just debug. Following up, Omega Metroid fight is mainly normal until you absorb the X for the SA-X, nothing happens except Samus regains all health then the Omega Metroid stops working
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