If we are still trying to guess, i'd say its 'Amber', specifically from a point in time after paragon and renegade route collapse into each other.
Why:
First i question if Madam X is actually actively trying to stop the MC, which is somewhat ambigious, since while standing in our way sometimes, she also saved us some times. Now why is that. I could guess 2 possibilities: Either she is actually trying to help us out bc of previous relations, or she NEEDS the Mc to do certain actions until a point in time in the near future to ensure her own existence.
Now, if she refers to her father she probably talks about deagan (also had interactions with clear), who seems to be set up to be still alive altough injured. The way WLL and in the maingame his role was highlighted seems very suspicious to me. She might meet him after the (failed) Raid.
The Raid, we know from some Dialogue by Melia has failed in some Timelines, however it seem Amber isn't planned to participate in it. Now when she said her Mother (Tesla in her case) died protecting her, could this happen during the release of Xenopurgis / the Rift Stakata? Maybe. She could have gotten the Soulstone from whatever was left of the squad around the MC after the Raid . (Since Timetravel via different Routes seem to exist, Cause and effect don't necessarily have to play out in Order). There are some more things; At the beginning She doesn't seem to recognize the MC, but we also know from the School of Nightmares that the MC looks different to everyone in the Main Cast, so the MC could have a Form she didn't know up to that point.
Kieran and Clear also talked about their Master (who could also have been Varya possibly) but the Name was garbled out. Garbled out like a Character hit by the Obliteration Spell...and well, who got hit by it?...
On the Paragon Route MC gets a Letter from Amber, and if we ignore for a second its just her soaping up for the MC a bit, what if in this letter is an actual explanation for some of whats going on? Also, at the Time of the Concert, she also has flashbacks from the doomed timeline. Madame X Armor was argued to prevent overlapping, which would be needed in both doomed and 'our' timeline, but also as seen by MC and Melia, overlapping doesn't happen in an instant, so there is some time before correction occurs. Now would correction also happen for a character that was 'Erased'?...
Now what would the Motive for that MadameX be...Since that Amber would have experienced both Paragon/Renegade and Doomed Timeline all ending up more or less Hopeless, she could act as a new 'Variable' in the entire Chain of Events to create a different Outcome. Until a certain Point After the Raid, her goals (to result in her existence) would coincide with Kieran and Clears Objective. There is also how Clear kinda guided Keta away from Tesla to Taelia in WLL, resulting in both Amber and Aelita existing how they are, both being needed (Aelita for Amethyst Grotto maybe).
If i'm right so far, i speculate that Renegade and Paragon Routes repeat after each other in a loop with only Melia escaping via the Paradox Gate, since the Plains of Dissonance Renegade ended pretty much where the Plain of dissonance Paragon route starts (Melia chasing after Aevis with a metal Rod and getting the situation turned on her, getting knocked out, only to awaken with the Paragon Melia Mind, getting dragged indoors by Aevis), It seems that on Paragon Route, Melia gets also switched for some slightly different Version of herself after interacting with the Pillar, altough not as extreme as M2. This Melia creating the Obliteration Spell, which M2 didn't even understand at first...
Possible Logic Holes: I have no fitting explanation where she got that yvetal, maybe showed up after witnessing basically all her friends and family dead, idk...
Locations: Some Locations wouldn't make much sense (Madame X Armor facility at amethyst cave?) but when you think where darchlight manor and Zone Zero are located on the map, in the past and present, i don't weight location accuracy that hard anymore...
Also the MC being required for Amber to become Madam X could make the Joke Ending of MC leaving for Hoenn at the beginning become canon as a previous reset Timeline...
If we are still trying to guess, i'd say its 'Amber', specifically from a point in time after paragon and renegade route collapse into each other. Why: First i question if Madam X is actually actively trying to stop the MC, which is somewhat ambigious, since while standing in our way sometimes, she also saved us some times. Now why is that. I could guess 2 possibilities: Either she is actually trying to help us out bc of previous relations, or she NEEDS the Mc to do certain actions until a point in time in the near future to ensure her own existence. Now, if she refers to her father she probably talks about deagan (also had interactions with clear), who seems to be set up to be still alive altough injured. The way WLL and in the maingame his role was highlighted seems very suspicious to me. She might meet him after the (failed) Raid. The Raid, we know from some Dialogue by Melia has failed in some Timelines, however it seem Amber isn't planned to participate in it. Now when she said her Mother (Tesla in her case) died protecting her, could this happen during the release of Xenopurgis / the Rift Stakata? Maybe. She could have gotten the Soulstone from whatever was left of the squad around the MC after the Raid . (Since Timetravel via different Routes seem to exist, Cause and effect don't necessarily have to play out in Order). There are some more things; At the beginning She doesn't seem to recognize the MC, but we also know from the School of Nightmares that the MC looks different to everyone in the Main Cast, so the MC could have a Form she didn't know up to that point. Kieran and Clear also talked about their Master (who could also have been Varya possibly) but the Name was garbled out. Garbled out like a Character hit by the Obliteration Spell...and well, who got hit by it?... On the Paragon Route MC gets a Letter from Amber, and if we ignore for a second its just her soaping up for the MC a bit, what if in this letter is an actual explanation for some of whats going on? Also, at the Time of the Concert, she also has flashbacks from the doomed timeline. Madame X Armor was argued to prevent overlapping, which would be needed in both doomed and 'our' timeline, but also as seen by MC and Melia, overlapping doesn't happen in an instant, so there is some time before correction occurs. Now would correction also happen for a character that was 'Erased'?... Now what would the Motive for that MadameX be...Since that Amber would have experienced both Paragon/Renegade and Doomed Timeline all ending up more or less Hopeless, she could act as a new 'Variable' in the entire Chain of Events to create a different Outcome. Until a certain Point After the Raid, her goals (to result in her existence) would coincide with Kieran and Clears Objective. There is also how Clear kinda guided Keta away from Tesla to Taelia in WLL, resulting in both Amber and Aelita existing how they are, both being needed (Aelita for Amethyst Grotto maybe). If i'm right so far, i speculate that Renegade and Paragon Routes repeat after each other in a loop with only Melia escaping via the Paradox Gate, since the Plains of Dissonance Renegade ended pretty much where the Plain of dissonance Paragon route starts (Melia chasing after Aevis with a metal Rod and getting the situation turned on her, getting knocked out, only to awaken with the Paragon Melia Mind, getting dragged indoors by Aevis), It seems that on Paragon Route, Melia gets also switched for some slightly different Version of herself after interacting with the Pillar, altough not as extreme as M2. This Melia creating the Obliteration Spell, which M2 didn't even understand at first... Possible Logic Holes: I have no fitting explanation where she got that yvetal, maybe showed up after witnessing basically all her friends and family dead, idk... Locations: Some Locations wouldn't make much sense (Madame X Armor facility at amethyst cave?) but when you think where darchlight manor and Zone Zero are located on the map, in the past and present, i don't weight location accuracy that hard anymore... Also the MC being required for Amber to become Madam X could make the Joke Ending of MC leaving for Hoenn at the beginning become canon as a previous reset Timeline...