The Enigma Manip

The enigma manipulation refers to guaranteeing the Enigma Cannon shot at the space colony successfully destroys it, unlocking the final stages with Zero still a playable character.

Normally, even if you defeat all 8 mavericks, there is a small chance the colony is not destroyed, resulting in not being able to play as Zero for the remainder of the game (at least until a new game is started).

There are two known manips. Neither counts against In-Game-Time. One is significantly faster for Real Time, however only has a 4 frame window. The other is trivial to execute except the significant Real Time needed.

The RNG Manips

Intro Stage Demo

This is faster RTA but has tighter timing. You must press start to end the demo at a specific point.

Mattrex Demo

It takes longer to see the Mattrex Demo, since the game will play other demos first, however the Mattrex demo has a very easy place to end the demo for success - watch the whole thing.

That's it. Watch the whole demo, don't press start until you see the title screen again. Then continue your game and go immediately to the Enigma Shot.

How do the manips actually work?

The Enigma cannon succeeds or fails on a variety of factors, however these are ultimately controlled by the game's current "RNG" value. The game's randomness is set to a known value when a stage starts, then changes based on the events that follow. This value sticks through the stage selection screen, where the Enigma Cannon (and the Shuttle, if you get there) ultimately checks it for success against the Space Colony.

The manip works because of the title screen demo.

Just like normal gameplay, the demo screen itself sets the RNG value to known values at beam-in, and progresses it "normally" as the demo plays itself out. As such, it always lands on known RNG values every time it plays out.

The places mentioned above, the 4 frame window in the Intro Stage, and watching Dinorex to completion, are both RNG values where it is a 100% success rate for the Enigma Cannon even without upgrades (that is, with 0 mavericks defeated). 

In theory, there are likely other places the manip could work. However, these are the best two - one is fast RTA, the other is extremely reliable.