Standup Glitch
This page will explain how the stand-up glitch works and how to properly utilize it.
The stand-up glitch allows Samus to stand up and then move around during the cutscene after rainbow beam, which will allow you to deal damage to the health of Mother Brain's third phase.
The normal way to perform the glitch requires Samus to have a minimum of 700 Energy Tank energy on the frame that rainbow beam connects. Reserve Tank energy does not count.
There is an alternative, unorthodox method that involves shinesparking at the right time before rainbow beam connects, so that the stun is removed from the shinespark crash animation. 700 Energy Tank energy is not required with this method.
After the rainbow beam has ceased, you can force Samus to stand up by mashing directional pad inputs.
If your energy is above a certain threshold after rainbow beam subsides (which will be the case if you have Varia Suit active), you will need to damage yourself for the cutscene to progress. Mother Brain's leg is an ideal damage source, since it does not grant invulnerability. Note that you do not need to have Varia Suit disabled to perform this glitch, it simply makes it less risky. This is because after the first rainbow beam with Varia Suit enabled, if the player does not damage themselves quickly enough, Mother Brain will decide to fire another rainbow beam due to Samus having too much health, which can be disastrous.
The game will attempt to reapply the kneeling pose upon Samus at the moment the Super Metroid appears on screen to attack Mother Brain, as well as the moment the Super Metroid detaches from Mother Brain's 'corpse.' You will want to be airborne during these moments to avoid this reapplication.
If you are forced back into a kneeling pose after standing up, a single activation of the X-Ray Scope should free you. Alternatively, if you are close enough, being struck by Mother Brain's leg should free you as well.
Mother Brain will be given the health of her third phase the moment she becomes fully gray (right before the Super Metroid detaches). It is pointless to fire beam shots at her any earlier than then.
Mother Brain's third phase has 36000 health, which is equivalent to 40 charged Ice/Wave/Plasma shots. It can be difficult to output that many charge shots into Mother Brain before Hyper Beam is gained, but you can consistently come very close, to where you would only need a couple of Hyper Beam shots afterward to finish her off.
You will want to be cautious of your positioning when the Super Metroid attempts to detach from you. It will attempt to do this once you reach full energy again, and can also detach frequently during the remaining cutscene duration while you are moving around. Depending on where it detaches, you may softlock the game due to Mother Brain not being able to kill the Super Metroid with her rings.
You will also want to be cautious about firing the beam during the moment in which the Super Metroid starts exploding, as well as the point in which Hyper Beam is gained (the room becomes lit again), as during these points, the beam can cause the game to lag a tremendous amount - so much so that the game may never resume normal speed, effectively bringing an end to your speedrun.
You should be able to squeeze in up to seven charge shots after the Super Metroid starts exploding, but before Hyper Beam is gained. If you want to be safe, do less.
Wait until the room becomes illuminated to start firing Hyper Beam to deal whatever remaining damage you need to deal.
