           So looking at the different explanations for Phantoon, one could play with the idea of it being Mother Brain’s ghost because with the discussion of clones and cycles, it’s Mother Brain seeing herself being replaced. It’s that existential horror come true and now she is dependent upon and subservient to this clone that is like a daughter. She’s not even the main threat this time. It’s a helpless rage that attempts to reassert itself and eventually does!
           For this is not clarified within Super itself, it’s just hinted that there’s some connection between Phantoon and Mother Brain. But then at the end of Other M, which is all about Mother Brain having been cloned, it’s made explicit at the end that this isn’t even the first clone Samus has dealt with when the original returns and reveals herself as Phantoon. And even she was just a clone of the original Chozo known as Mother Hand who was used as the template for Zebes’ administrative AI.
           So it’s the ghost of Mother Brain and who she once was, she’s haunting Samus and even herself, her own past failure haunts her and is isolated to the wrecked ship. I presume Mother Brain was built on Zebes with how intertwined she is with its infrastructure and I like the idea that she was only able to be resurrected at all because Tourian is her true form as one giant computer and Mother Brain herself is like, a central processor within it. But idk maybe her failure to pilot the ship led to them landing on Zebes and Mother Brain is haunted by herself and who she was because that’s the point, she’s a victim of temporality.
           The other idea is that Phantoon is a parallel to the infant Metroid; Some sort of strange floating round creature with a toothy maw at the bottom that feeds on energy. It feeds on Mother Brain’s psychic energy and she manipulates it to guard one of the keys needed to unlock Tourian. If the narrative purpose of her return is to be jealous of her own daughter being a better mother than her by sabotaging that, then Phantoon is her abysmal attempt at one-upping Samus perhaps.
           Phantoon doesn’t care. Or maybe it does. Or it only cares because she was a source of food. It sensed Melissa Bergman from across the galaxy and by the time it arrived to suckle on its mother's nourishment once more, she already got merked by the Galactic Federation so it turns its attention onto Samus. A child avenging its mother who fed it, VS a mother who avenged her child after its final act was feeding her. After Samus, a mother, avenged her child and watched a mother fail to protect her child in Madeline Bergman.
           Of course, Other M suggests that Phantoon caused the Chozo to crash onto Zebes in the first place so it's likely older than Mother Brain. But given she already plays as a mother to Chozo older than her because of the elderly becoming dependent like children all over again, it could make sense!
           As it stands, Phantoon is so out of place for a final boss, it’s worse than Sylux in Beyond or Proteus Ridley in Samus Returns, so giving it that narrative/thematic connection to Mother Brain that was alluded to in Super is the only way to make it make sense. Of course, I do like the thought of salvaging Proteus Ridley by simplying having his encounter be a story set during Samus’ return to Federation space and he ambushes her during a pit stop on some random world. So maybe Phantoon can be the same.
