Alternate second half
If you let the colony collide with the Earth (let all the time run out), an intermission where Zero is infected with the Sigma virus and becomes a powerful Maverick will appear. For the rest of the game you cannot choose Zero and the dialogue changes for a few of the intermissions. Also, Zero fights more aggressively and uses different attacks when you fight him in the third Maverick level.
To get this faster, launch the shuttle before you have collected all the parts for it. This will also display an intermission where Zero goes Maverick and gives you the ending where X's memory of Zero is wiped clean. What you do with the Enigma does not matter.
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