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I have finished watching Tokyo Ghoul: Root A, but I am confused because when I saw the first episode of Tokyo Ghoul:re, Kaneki was in the CCG.

What happens after Kaneki carries Hide and meets Arima?

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The anime did not follow the events in the manga, hence the confusion. I am not sure when this will be revealed in the anime since some of what I'm about to mention have been revealed during the Rushima Landing Operation in the manga. Spoilers ahead!

What happens after Kaneki carries Hide and meets Arima? In the anime, Kaneki carries Hide towards the CCG and then Tokyo Ghoul:re suddenly starts with him as a CCG investigator. The manga's events are somewhat different and this was all eventually revealed.

  1. After his fight with Amon during the Owl Suppression Arc,

he met Hide. Hide tells him that he knew all along that he was a ghoul and that he wants to help Kaneki. This was all his memory could remember but it was revealed later on that he attacked Hide, hence he was able to heal himself and at least give a fight to Arima when he regained consciousness (Volume 14 Chapter 136).

  1. When Kaneki regained consciousness,

Hide was no longer there. He had a fight with Arima but was defeated. In the last chapter, Kaneki’s suspect profile is shown to have been erased from the blacklist. (Volume 14, Chapter 143)

  1. In the epilogue,

Kaneki (now Haise), met Akira Mado for the first time while she was visiting her father's grave.

  1. Since Quinxes were already present prior to the start of Tokyo Ghoul:re, it was said that the Quinxes are a result of the CCG examining and, possibly, performing experiments on Kaneki's body after his fight with Arima.

  2. In Volume 7 Chapter 67 of Tokyo Ghoul:re,

it was revealed that Kaneki was kept in a prison cell after the events of the first manga. He was alive but he seems 'crazy'. During his time here, he forgot his identity (in the manga, it was depicted that during his crazy tantrums, he started questioning where he is and who he is). It was here that Arima asked him to pick two of his favorite kanji that will be his name (this was where his name 'Haise' came from) after revealing that the Rehabilitation Program has plans for Kaneki to be an investigator (this most likely happened after he was experimented on).

The anime skipped many parts and events in the manga. I suggest you read it or Season 3 would be confusing to watch.

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