The Hatchling
"I paid you back."Yo' Mamma
If you people remember back in the 90's Super Metroid came out, which still surpasses all other Metroid Games. However, do you remember the hatchling that you found on SR388? Well, you had to rescue it from the Pirates, right? That is what Hatchling is, her "daughter".
The events happen the same in the movies, but something else happens. When a Metroid hatches, it slowly evolves to its mothers likeness. Well, Hatchling slowly grows more "human" in appearance; and over time, it evolves to look like the Hunter, Power suit and all.
It retains the information for Samus' Suit and weapons from the Space Pirates. They hooked her up to life monitors while she was hibernating to see how she was evolving. However, she found a way to hack into the main database to steal their research and develop her own. So now she knows everything the pirates know, even the Mother Brain's weakness...
The Hyper Beam
The Hyper Beam will be created in the last battle in the movies. When Samus is downed from Mother Brain, Hatchling comes and returns her side of the favor. She fights valiantly with the mecha-brain, but is soon killed. Her blood, however, slithers up to Samus and whispers to her telepathically, "I paid you back..." I'll let you figure out why she said that.
Next, Hatchling's blood seeps into Samus' bloodstream and her power suit, making her replenish her energy, and creates the Hyper Beam. It is the most powerful weapon in the universe, so it drains the power suit from Samus.
Ill let you imagine what happens next. It will be revealed later...