Beware, if you haven't watched the anime Sword Art Online
yet, this post contians many spoilers. Proceed with caution!
So, p2 got me to watch Sword Art Online.......and some things just didn't add up or sticked out quite a lot.
Let's start with Yui: What do we know about her according to the series? She's an AI developed to help players mental state not drop too low. However, something doesn't add up here, she is way beyond any other AI we see in any part of the universe, in any game whatsoever. She feels way more natural, way more human-like when talking. We have seen how other AIs behave in the Calibur story arc (Season 2 episode 15-17) and Yui behaves way more advanced than those. However, we have indeed seen one more artificial intelligence with a similar level of human-like appearance: Kayaba, but more on that in a bit.
Yui also seems to be spreading around like a virus: She copies her code everywhere, all the time. While in SAO Kirito transformed her to an object and the player data got copied over to ALO she said at the end some time that she copied her source code over to Kiritos NerveGear, so that even if ALO would end Yui would live on. Afterwards we see still see her in virtual reality, even after Kirito stopped using his NerveGear and started using an AmuSphere, so Yui had to copy herself multiple times around. Yui is also still able to interact with the virtual world even if Kirito isn't around (Look at the GGO story arc).
So, since I just mentioned Kayaba, let's take a closer look at him: after Kirito cleared SAO he "uploads" his brain to live on as an AI-kind-of-thing, while, in the process, melting his RL brain. We know for a fact that he dies right at the end of when SAO is cleared IRL, like that one bartender guy said. The bartender guy also said that some people say it was suicide. We know that Kayaba successfully created an AI ghost thing of himself as Kirito meets him at the end of ALO. So long story short: we know that brain-uploads to AI are indeed possible.
Yes, in case you already caught on, I am kind of implying that Yui is actually a real person who's brain has also been "uploaded", just like Kayaba. But who and why? How does this fit in with any of the story? Before we get into that, let's talk about the seed a bit. But even before that we need to look at the game SAO a bit closer.
SAO was built by Kayaba to trap every player inside. Once that happened the company running SAO faced multiple lawsuits and went bankrupt, a different company took over the hosting of the SAO servers to keep the players still hooked up alive. (I think this was Season 1 Episode 15) But why would a for-profit company do such a self-less act? Well, in fact it wasn't too self-less, they quickly took the SAO programming and started to modifying it, out came Alfheim Online (ALO). We know that because as soon as Kirito releases Yui in ALO she says that the engine and player data seem to be almost identical with that of SAO. But when got ALO released? IMO it is quite clear that ALO got released before
Kirito cleared SAO, here's why: For one, Kiritos "sister" said in a flashback she wanted to know what her "brother" got so much into VRMMORPGs that he got himself locked up for such a long time. While not directly mentioned it seems to be implied that that flashback happened before Kirito cleared SAO. So she started getting into ALO. Then, additionaly, the company that took over the SAO servers is the same one which runs the ALO servers. As already mentioned, they are a for-profit company so they need some kind of benifit: just running servers doesn't give them such a benifit, so they had to counter that by making some money. The easy route was to just take SAOs engine, add the logout feature, fix the hardware, and make a new world: ALO. That is exactly what seems what they have done, so that they could earn money which could also pay back the SAO servers while still giving them more profit. So I'd say it is pretty fair to say that ALO was released before Kirito cleared SAO.
So, let's start tying some lose ends togeather, shall we?
Let's just say that Yui was indeed a real person who's brain got "uploaded" and transformed to an AI-like thing, such as Kayaba did, then who and why? Let's say that YUI was IRL somebody Kayaba really cared for, a loved one, his wife, or maybe his daughter? Let's go with daughter for now, since that seems to fit best.
Now let's say that Yui had some kind of deadly illness or something and it was certain she would pass away, Kayaba being her father would of cource not want that to happen, so he goes to the only option he thinks is left: Upload her brain and create an AI out of her, so that she can still be around enjoy the world, even if her physical body is gone. However, that also requires a world to be present, and that is how SAO is born.
Now hold on soru, there are tons of things not working out here, such as why would it take so long for her to appear in the game, why is she a mental-health-assistant AI in SEO? Why would Kayaba make so many players trapped in SAO? This makes no sense?!
Ok, so let's get at this one at a time:
Why would Kayaba make so many players trapped in SAO? Well, if Yui would see other players die and just re-spawn, she might pretty quickly think that she isn't part of them, that she doens't belong, and such a life isn't a happy life. She can know the truth, but maybe when she's ready, when she's a bit older?
Now, for the others, bear with me for a bit: Kayaba loved Yui, so he wanted the best for her, however he knew that if she would just be dumped from the beginning into the game other players would quickly notice that she isn't like them. She is just an AI, is not a normal interactable player, other players might even try to slice her up! That explains why she is an immortal object. Yes, Cardinal, also developed by Kayaba did try to destroy her, more on that later.
So, why isn't Yui just an immortal object and present from all the beginning of SAO so that she can experience the world as much as possible? While she may be an immortal object, that wouldn't mean that some players would try to kill her at first. That might traumatize her. On top of that, if there is this NPC you met in the beginning of the game you would probably never go back to it, ever. So Yui would have a pretty lonely life - not what Kayaba intended.
So Yui had to wait for the right moment to appear, but when is the right moment? This is where Kirito and Asuna fit in: Yui needs protection from real players, she needs to experience love and be protected by players to be able to have a happy life, she needs a momy and a dady! But how could she find such people if she isn't part of the game, can't interact with it? Well, that is why she is an AI to monitor the mental stability of the players: She is able to sense if the other players are happy or not. (Hiding as such an AI probably also helped her to hide from the error correction program which almost kills her later on.) This also explains why she is not able to interact with them and had to watch all the depression - if she would have been able to interact with the players all the time then she would have never started having a momy or a dady, she would have get used to the depression of all the players or maybe some players would start to discriminate her when showing up! Remember: she had to pick the right moment. So she was able to sense the imense love of Kirito and Asuna, and finally tracked them down and was able to interact with them. But why would she have amnesia? Well, Yui needs protection. So she needs to find people who care for her. So essentially she gets Kirito and Asuna to care for her, by being this helpless girl with no memory. And did it work? For sure it did!
That was a lot, so lets recap before moving on:
- Yui was the daughter of Kayaba and was dying, Kayaba wanted to create a world for Yui to live in, which would become SAO
- Yui needed protection, which is why she was able to sense others emotions and find the happy ones and find protection with them (Kirito + Asuna)
- Yui needed to wait for the right moment to appear, that is why it took so long for her to appear in the series
- Yui couldn't interact with the world prior to that for her own protection
Ok, so that that is out of the way, let's see how well this fits in with the rest of the story!
Heathcliff (Kayabas avatar) was probably concerned about Yuis fate and checked with Cardinal every now and then to also look at the mental states of players, to pick the happy ones and maybe take a closer look at them, to see if his master-plan to save Yui was working out. That is how he found Asuna and how she became second in command for Knights of the Blood, that way it was a breeze for Heathcliff to keep a close eye on her. He probably learned about Kirito earlier on, too, but it was way harder for him to keep a close eye on Kirito, as Kirito played solo. Eventually he did manage to keep a close eye on Kirito by Forcing him into the Guild. Keeping an eye on Kirito was so important to Heathcliff that he did risk revealing his true identity being Kayoba in doing so (by using special attack stuff in the dual which shouldn't be possible for a player). So why would Heathcliff approve Kirito+Asuna's vacation then, when he wanted to keep a close eye on them? Maybe he realized how much they loved each other and wanted to see how they behaved on their own, maybe that would trigger Yui's radar and get her to finally join this world (and that did happen after all). But of cource Heathcliff wouldn't just leave them go without still supervising them, after all, the life of Yui dependet on it! But using Cardinal it would still have been possible to keep an eye on those two, while actually being a bit harder, it'd still be possible.
OK, so Kayabas plan did work out: he saved Yui and managed to get protection for her in SAO. But what about after SAO? That is where the seed comes into play. You can easily view the seed as the basic engine on which SAO runs, that means that ALO also runs on the seed, and since Kirito released the seed (You could think of it as open-sourcing the engine) basically every VRMMORPG runs on the seed, such as GGO. So that means that as long as the seed is around Yui would have a world to live in! That's great! But wait, why would he himself not release the seed then? Why would he risk losing Yui like that? Perhaps because Kayaba didn't trust people, he wanted to make sure Yui was in good hands. And he had to watch a bit longer.
Kayaba probably knew that if he came out of SAO alive he'd be facing tons of trials , probably go to jail and all-in-all would be unable to watch and help Yui. So, after Kirito defeated him and their little talk in the sky he also uploaded his brain to also become an AI thing. But why wouldn't Kayaba tell Kirito the reason why he created SAO then, after Kirito ask? Again, to protect Yui: Kayaba wasn't for sure at that point if Yui was with Kirito or not, he probably had other suspects, too, and he simply didn't know where Yui was. So he couldn't risk Yui like that, if the story would have been made public people would out-cry and start disliking Yui, with stuff like "4000 people died IRL to save a virtually dead child?!" So he had to say that it slipped his mind, why he created SAO.
Then, why didn't Kayaba do anything himself with the seed, after all, if SAO was over all the data would be gone, and along with that Yui! Well, we know that after Kirito cleared SAO all the data was transfered to ALO. Kayaba probably knew of ALO, since he had access to Cardinal, and if such a transfer could happen so quickly there must have been some kind of link before that, thus Kayaba already knew Yui would still be safe, even after SAO was gone. That is also where Kayabas brain-upload-ai-thing went.
So, we are almost there, if you have read this far, thanks for sticking around ^.^
Now, at the end of ALO Kayaba actually sees Yui with Kirito, and it isn't the first time Kayaba sees how much Kirito would do to protect and help loved ones. He also saw how Yui called Kirito "dady" and Asuna "momy", so Kayaba knew for sure that Yui was in good hands with Kirito and Asuna, they wouldn't hurt her at all, she would have a happy life there! However, they were in ALO, some game that was being controlled by some weird femenizing maniac....that is why Kayaba gave Kirito the sead, so that Kirito would be albe to create own worlds, Kayaba had seen multiple times how caring Kirito was so he knew he could be sure that he'd protect Yui, no matter what. Kirito was OK to have power over the seed. Yui was safe with Kirito+Asuna. Kayabas job was finally done! He managed to save Yui!
But, hang on soru, you mentioned something about Yui having virus-like behaviour at the beginning of this way-too-large post? How does that fit in? That is quite simple: That is human behaviour, Yui knew that is the only way for her to survive, if she got copies of herself all over the place, so that is what she did!
So, to sum it up, Kayaba sacrificed the lives of 4000 random people to save the life of his almost-dead daughter.....
But hey, that's just a theory.....an anime theory....aaaaaaaaaaaaaaand cut!
EDIT: Oh, I forgot to mention, thanks a lot to @p2
for helping me out with specifics how it fits into the story!
You forgot to mention how Kayaba developped the medical device based on the nervegear (or on which the nervegear is based on?) which was then part of the 4th storyarc. This is another strong hint towards him caring for a person in critical medical condition, trying to improve their live (probably this is how it all started? HIm trying to save a life unsing this, losing her, moving her conciousness inside the system, then creating the nervegear for the public?)