Sword Art Online's third season has started the War of Underworld arc with a Kirito looking much worse for wear than ever before. Although he began his jump into the Underworld under dire circumstances since his body was afflicted with a terrible poison, he's currently facing trouble both in the real and virtual worlds. The premiere for the new arc revealed a Kirito that somehow still has retained his bodily functions, but Alice mentioned that Kirito has lost all of his emotions along with his ability to speak. But the latest episode of the series explained just what's happened to him after the fight with Administrator.
War of Underworld's second episode broke down the complicated situation Kirito is in that began with the initial glitch of when he first dove into the Underworld with all of his memories of his real world self. Essentially, when he tried to contact the outside world after the Administrator fight, a power outage caused a short circuit to his virtual self.
As Higa explains, Kirito's in the worst-case scenario. After the poison attack left Kirito's neural network damaged, Raft had begun his treatment by blocking his memories and sending him into the Underworld. But an error caused him to be uploaded with the complete knowledge that he was in a virtual world that's currently in an accelerated timeline. Although not long has passed since he began in the real world, he's been in the Underworld for two years.
When he tried to contact Raft through the console in the Central Cathedral after Administrator was defeated -- which he did in order to save the Fluctlights in this world from being deleted after his recovery and return to the real world -- a power surge caused his Fluctlight to short circuit. Because he was blaming himself so harshly for Eugeo dying, the short circuit followed through on this by deactivating his "ego."
So now Kirito's virtual self has a tiny black hole in his mind where his decision making processes should be. His body is unharmed, but all he can do is reflexive reactions based on deep memories. It's why he kind of goes off the rails when separated from Eugeo's sword, and occasionally shouts at night. He no longer knows who he is, what his mission is, or can speak on his own.
Until Kirito can somehow fix himself, Alice will continue to struggle in the virtual world and out. There are mercenaries after her fluctlight, and now Kirito can't remember that he's supposed to protect her. Which means the War of Underworld arc is a lot more layered than initially expected. If you wanted to jump back into the series, you can currently find Sword Art Online: Alicization - War of Underworld streaming on Crunchyroll, Funimation, HIDIVE, and Hulu.