Hyper Beam is gifted to Samus after the "Baby" Metroid perishes from Mother Brain's assault during her third phase. It deals 1000 damage to all targets.
It shares a very similar appearance to charged Plasma Beam, with the obvious difference being the rainbow color effect involved.
Like Wave Beam, it can pass through surfaces, and like Plasma Beam, it can penetrate targets.
It can destroy objects certain other beams and items normally cannot, such as the gates that come down in the first room of the Tourian escape.
Hyper Beam has a cooldown of 21 frames, meaning it will only fire once every 21 frames. It will automatically fire at this rate if the shot button is held.
It can still be used in conjunction with Space Time Beam if a space time particle is created before Hyper Beam is gained.
In a scenario where you land on Ceres Station with Hyper Beam (ex. using space time to take Hyper Beam out of Mother Brain's chamber, saving the game, and reloading the save, which will cause the intro sequence to play again), Hyper Beam will be removed and replaced with Charge Beam, Wave Beam, and Plasma Beam.