Deeper Layers is the fourth installment of Tokyo Ghoul Root A. Aogiri storms the Cochlea prison, freeing inmates and slaughtering guards, while Amon confronts the ghoul who raised him and Kaneki descends into cannibalistic instinct.
With Aogiri Tree gaining ground, Yoshitoki Washuu is pulled back toward the front lines and asks Itsuki Marude to serve as his deputy, despite the failed campaign in the 11th Ward. Still lacking any lead on the Owl's true identity, the CCG turns to an imprisoned ghoul called Priest and dispatches Koutarou Amon to question him.
The interrogation stirs Amon's memories of the orphanage where Donato Porpora once cared for him. As a boy he stumbled onto Donato feeding on a dead friend, and he has never understood why he alone was spared. At Cochlea, Akira Mado presses him on the reason for the visit but gets no answer. Donato claims ignorance about both Aogiri and the Owl, and only as Amon turns to leave does the old ghoul remark on the crucifix he now wears in memory.
Aogiri then assaults the prison. Freed inmates side with the attackers against the guards and investigators. Ayato Kirishima and Ken Kaneki push down through the levels before splitting off, while Tatara and Noro cut through personnel as Eto looks on with delight. Kurona and Nashiro Yasuhisa slip inside hunting for Kaneki. Cornered by Naki and the twins Gagi and Guge, Akira wounds Naki with her chimera weapon Amatsu and releases a suppressant gas grenade that saps every nearby ghoul's kagune, though Naki still bites her leg. Amon refuses to abandon her and hauls her clear of the swarm.
Answering a call for help, Yukinori Shinohara and Juuzou Suzuya reach the prison. Juuzou runs into Kurona and Nashiro, who once knew him as Rei and resent seeing him again, and he goads them toward a fight. Ayato clashes with Shinohara, growing enraged once he recognizes the quinque Arata as a weapon made from his own father. Deeper down, Kaneki frees Shachi, who attacks after catching Rize's scent on him and overpowers him. Eto interrupts, luring Shachi away with the promise of seeing Rize and leaving Kaneki stranded among corpses, where his hunger drives him to devour the bodies and awaken his kakuja.
Yoshitoki returns to active command and names Marude his second. Amon interrogates Donato and confronts the memory of his childhood under the ghoul's care. Aogiri raids Cochlea, releasing prisoners and overwhelming the guards. Akira injures Naki but is bitten, and Amon carries her to safety rather than leave her behind. Ayato recognizes Arata as his father's remains and turns on Shinohara with fresh fury. Shachi is freed and defeats Kaneki, then departs with Eto, after which Kaneki cannibalizes the dead and triggers his kakuja transformation.
The episode draws on manga chapters 82, 83, 91, 97, 100, 101, and 104, with several scenes rearranged. Together with the following installment, it compresses the Second Cochlea Raid together with the assault on Kanou's laboratory into a single thread. Root A withholds Kanou's real aims and Rize's surviving body, only hinting at them. In the source manga the pair take on both Tsukiyama and the White Suits, whereas the anime limits their fight to Naki and his crew.

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Episode 16, "Deeper Layers," is not a filler episode. It adapts manga chapters 82, 83, 91, 97, 100, 101, and 104, though several scenes are rearranged and compressed with the following episode.
In "Deeper Layers," Aogiri Tree storms the Cochlea prison, freeing inmates who turn on the guards and investigators. Ayato Kirishima and Ken Kaneki push through the facility together before splitting off, while Tatara and Noro cut down personnel as Eto watches with delight.
Amon questions Donato Porpora, the ghoul called Priest, because the CCG has no lead on the Owl's identity. The interrogation also stirs Amon's memories of the orphanage where Donato once cared for him as a boy.
In Episode 16, Kaneki frees the ghoul Shachi, who attacks him after catching Rize's scent and overpowers him. After Eto lures Shachi away and leaves Kaneki stranded among corpses, his hunger drives him to devour the bodies and triggers his kakuja transformation.
Cornered by Naki and the twins Gagi and Guge, Akira Mado wounds Naki with her chimera weapon Amatsu and releases a suppressant gas grenade that saps every nearby ghoul's kagune. Naki still manages to bite her leg before Amon carries her to safety.
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