I have always been wary of the theory that Madame X is Kenneth/Keta's daughter Nora Royer. X appears in close proximity to Keta in many instances across multiple timelines, yet she has never acknowledged him except at a business/formal level. In the Xen HQ in Ch2, where the player is transported to the Xen lounge, Madame X is in the background presiding over the meeting concerning Keta's death, yet she doesn't even acknowledge him. She authorized the building of the volcano base and blackmailed Keta, and it would have killed him even if he hadn't confronted Mewtwo, due to the eruption. Also, during the Doomed Timeline, she only acknowledges him as "the leader or the survivors", and pays no attention to any relationship. Should things go south and the player tries to escape, she doesn't care about any of the survivors, much less Keta. She only mentions the Interceptor not doing Xer job. Even if she was brainwashed and raised by Clear/Freya, Nora could still recognize Keta in WLL, and seemed rather fond of him. Also, X oversaw Blacksteeple and let Neved torture Aelita, which was originally intended for Keta and otherwise enabled his vendetta against Keta. My personal theory is that she is the daughter of Team Xen's founder, just as Giovanni in RBY is the son of Team Rocket's founder, both of which are dead but whose organizations live on. Being Melia/M2 or Erin doesn't make sense as Madame X never goes after Erin despite being a member of the Archetype, and her interest with Melia seems to be related to Vitus/Indridad, and neither Melia nor Erin overlap with her or even show the symptoms despite the proximity, as it is stated that M2 and Madame X are separate individuals in Renegade. There are just my thoughts, feel free to comment. I have only played up to 13.5 Renegade, Florin dead and Karrina alive, not Paragon yet.