Warning: This chapter will contain spoilers, as it will serve as a checkpoint for explanations about the protagonist's powers.
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Kakugan:
The Kakugan (the black eyes with red pupils from Tokyo Ghoul) are always "active," Kaneki's eyes will always be a different color, but the terror effect he has on people is something that can be controlled.
When I say that the Kakugan is active, I mean that this terror effect is active.
There is a visual change for the Kakugan to be active; the eyes develop small red markings, even extending out of the eyes and painting the skin. The image on the fanfic cover is a good example.
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Kagune:
The protagonist possesses all types of Kagune, including Rinkaku (Back), Koukaku (Arm), Ukaku (Shoulder), and Bikaku (Tail), all of which are red in color.
The Rinkaku is similar to Ken Kaneki's Kagune, meaning it has four scaly tentacles.
The Koukaku comes in the form of a gauntlet, with a shield on top and a spearhead (a blade) at the end.
Ukaku: ...
Bikaku: ...
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Images:
(If there's nothing here, it's because we haven't reached the chapters that contain images, or I forgot to include them :P)