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Or... Something... It helps to treat them as non-canonical... Where does Helba go into this much detail about where thy came from? The Subaru thing is interesting, but Sora was only ever one PC... Unless Helba has a blue Kite somewhere...

I believe she hints at it in her initial e-mail that I believe goes something like this "Perhaps they're real. Perhaps they're fragments. The truth is yours to decipher." Or something along those lines.

Where does Helba go into this much detail about where thy came from?

Analysis. >.>

"Perhaps they're real. Perhaps they're fragments. The truth is yours to decipher."

Yea, and Tsukasa still acts all emo despite having overcome that and still thinks he's a male, Subaru has memory problems and still thinks the Crimson Knights are active, and Sora can friggin' see the Bracelet.

Skeith took control of Sora. If you remember what Morganna said, "I will show you a fate far worse than Death" And then he gets DDed, Sora fell into a coma in the real world, but his mind stayed in the game. Skeith is so evil, but so cool at the same time!

I believe the AIs were generated through Tsukasa, Subaru, and Sora's contact with Aura...

As there are AI versions and then the players themselves, that means there are two of each.

Tsukasa's AI was born as a result of all those copies Morganna tried to make. The ones we saw in Net Slum. Helba supposedly deleted them, but they returned to the sea of data and came out, merged as a functional, whole clone of Tsukasa.

Sora's AI was born as a result of Skeith creating Shadow Sora in Zero, and then when it was destroyed and reconstructed as a normal Sora copy.

Subaru's AI was a result of holding Aura's hand at the very moment Helba unplugged Net Slum.

All three of them are accidental.