1

At the end of the first arc, Kayaba says that all the remaining players are safely logged out. In the next episode, we find out that isn't the case.

Why didn't Kayaba notice that a good number of players were still logged in via their Nervegears?

He clearly had admin access to not only the game, but the servers; was intimately familiar with the source code, the design of the Nerve Gear, etc.

Kayaba should have been able to notice anyone mucking about in the servers to prepare for such an event as to shuttle users from one VRMMORPG to another, especially because it was only him and Cardinal running the servers.

3

Because it's assumed his physical body died

In the aftermath of the death game, Akihiko proceeded with his desire to die along with the collapse of the game, as he had decided before Sword Art Online even began. He thus used a remodeled FullDive machine to perform a super high-powered scan of his brain to transfer his consciousness into the virtual world permanently. This scan led to his brain cells burning out, killing his body.

Source: Akihiko Kayaba > Chronology > Aincrad Arc (last paragraph)

now it's up to debate whether Kayaba's consciousness still lives but even if he lived on there's the fact he proably didn't care too much

Kayaba Akihiko had little to no empathy, with a complete disregard for human life, including his own, and instead was completely taken in by the virtual world. When he accidentally struck Asuna, which caused her apparent in-game death, he showed no remorse, and instead seemed rather amused, even though it caused Kirito an incredible amount of grief at the time. He chose to fulfill his dream by making a death game which cost thousands of lives, and simply noted that their minds were gone from both worlds. His fascination with computers was very much like Kirito's, with the major difference being Akihiko having no regard for the lives of others, and Kirito doing everything he can to protect them.

Source: Kayaba Akihiko > Personality (3rd paragraph

there's also the fact that Sugou knows the SAO systems because ALO is uses SAO's code base. also

Once «Sword Art Online» (SAO) was cleared, thus disabling the security of the SAO servers, he was able to hack into the SAO server via router and reroute the minds of three hundred SAO players including Asuna, to ALfheim Online.

Source: Sugou Nobuyuki > Background

i would assume Sugou would know to reroute the minds without drawing suspicion to or linking it back to the ALO servers or himself so even is Kayaba could do anything, it would proably be mitigating the damage (ie. less players get transfered). also Hollow Fragment would suggest that Sugou had Admin permissions in SAO as well so assuming Kayaba didn't have Super Admin anything Kayaba could do to stop Sugou he could just undo

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