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.
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 pressing up. To guarantee enough time for the next phase of the glitch, spamming up is recommended.
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.
After Mother Brain has fired 10 sets of rings at the Baby Metroid, the Baby will detach, move off the right side of the screen, then charge in for the final blow. Except if you have maximum health, as with 100% runs, in which case the Baby will detach just before an 11th set of rings. For this category you can bring the Baby to the top right side of the screen at this time to manipulate it into the cutscene earlier.
If you are changing pose on the same frame as one of the Force Stand conditions, you could get stuck in midair. This is most common when walljumping as the Baby Metroid comes on screen. If Mother Brain can't hit the baby from this position, it's a softlock.
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.
This form of softlock is particularly hazardous in GT Classic, since you have exactly 700hp to work with, so the Baby Metroid will finish refilling your health very quickly unless you damage yourself on Mother Brain.
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. If you are holding a charge when Hyper Beam is obtained, the game will lag tremendously. You can hold item cancel (or item select if an item in the HUD can be activated) to end the charge and clear the lag.
Wait until the room becomes illuminated to start firing Hyper Beam to deal whatever remaining damage you need to deal.