This plot line starts from around Tokyo Ghoul ch106, when Kaneki infiltrates Kanou's house and laboratory (or I think it's Cochlea in the anime's second series). It's after he goes crazy as a kakuja, has a confrontation with Shinohara, and then one with Amon.

'Just a ghoul!? That's all, isn't it?' Amon screamed at Eyepatch.

Shinohara was twitching on the floor. Suzuya was panting manically, his scythe in hand. Amon was staring at the ghoul that had fallen at his feet, as its destroyed kagune retreated into the exposed skin on its back.

'I don't…' said the ghoul, muttering into the floor. 'I don't want to eat anymore.'

Amon heard a sigh escape from his lips. In his world of black and white, of rules and regulations, this one thing before him was evermore blurring everything into a lowery shade of grey.

Eyepatch twitched. Then, faster than Amon could believe, it had pelted away across the room.

'He's running awayyyyy,' said Juuzou in that sing-song voice of his.

'Amon-San!' cried one of the supporting investigators. 'Shinohara-San is alive! It's mostly his armour that's been eaten…'

'Stay here, Investigator Suzuya. Protecting Shinohara-San is top priority.' Hoisting his quinque into the air, Amon gritted his teeth resolutely. 'I'll chase the Eyepatch ghoul.'

The grey walls were fast becoming a blur as Amon raced through them. Eyepatch had left a trail of destruction that was easy enough to follow. By the look of it, its kagune had already regenerated and had taken many a chunk out of the surrounding concrete.

Within minutes Amon could tell he was nearing the ghoul. Echoing crashes sounded in front of him, and as Amon turned a corner he saw the ghoul slip down through a vent.

Amon followed, which due to his size was more of a challenge, but he was soon through the vent himself and stumbling through basement tunnels that looked more than a little worse for wear.

Then the eyepatch ghoul was stopping, and turning around. It had heard Amon, and now it could see him.

'I have to protect everyone…' the ghoul said, almost screeching. Amon met this with a crashing roar and ran head-on at the ghoul.

The ghoul lashed out wildly with his kagune, and the surrounding walls crumbled where the limbs crashed into them.

It was all happening so fast. They both struck, and defended themselves, and struck again. Another crash, and now the falling dust didn't cease, and the ceiling began to fall.

Amon seemed to have blacked out momentarily as he was knocked to the ground and his quinque was sent flying out of his hands. When he came to he was covered in dust and completely surrounded by piles of broken concrete, brick, and iron framing. The long basement tunnel they were in had imploded, and been cut to only a dozen or so square metres, completely enclosed by rubble. The floor Amon was lying on seemed stable enough, and the position of the metal and ceiling seemed to be preventing a large part of the rubble from squishing him, but Amon was concerned about a much more imminent danger. He backed against the wall as the grotesque figure of Eyepatch loomed out of the dust.

Amon was wary of and utterly perplexed by Eyepatch's behaviour; it appeared utterly deranged. This ghoul had seemed so steadfast, so articulate and sincere when they had first met in the rain those weeks ago, but now it seemed it couldn't even make sense of their precarious situation. Its red, tentacle-like kagune was writhing about in the air as rambled words fell out of its mouth.

'Why did i throw away my humanity? I can't… Not anymore... sorry I'm sorry I'm sorry I'm sorry I'm sorry I'm sorry I'm sorry I'm sorry… Eating me… From the inside… insides… gently scrambled… 923… 916…'

Amon was terrified of what was before him, trapped with him under a pile of rubble, but there was one thing that could still give him the edge. His eyes swept the ground, searching everywhere for the glint of steel that would tell him his quinque was within reach. He was ready to cry with relief when he saw the edge of the briefcase poking out from beneath what looked like a cross beam, but the elation was short lived. Amon skirted across to it, keeping as much distance between himself and the lunatic ghoul as he could. He crouched down to try and pull the weapon free, but it was stuck fast under the debris.

He was trapped, weaponless, and otherwise utterly incapable of defending himself.

'No,' he suddenly heard a small voice say in the raving darkness. 'You always fight, even if it costs you your arms and your legs.'

Amon stood up determinedly and turned to face Eyepatch. The bold movement seemed to have notified Eyepatch of his presence, and the ghoul turned towards him as it knocked its head to one side.

'867… 860…'

It look a step forward, still muttering madly. Amon balled his fists as the ghoul approached him, but then it let out a yell of pain and clutched at its stomach.

'I can feel it… It's eating me…'

The ghoul's kagune was going wild, thrashing about and hitting off the already precarious ceiling. Amon, in what felt like utter desperation, crouched down and tried to tug again at his quinque, but it was no good. He heard a roar of utter anguish and stood up in time to see Eyepatch run forward. The ghoul jumped at Amon and latched its legs around his chest, its strong arms frighteningly close to Amon's throat. The impact of the hit sent them both falling to the ground. Eyepatch had its hands wrapped in Amon's suit and its face in the nape of Amon's neck, but where it had once taken a bite out of Amon's shoulder it was now just murmuring incoherently.

Trickling dust continued to settle, as Amon lay beneath the ghoul. The only sound was their heavy breathing, their rising and falling chests millimetres apart.

Amon didn't know what to do. He lay still for a moment, paralysed with utter shock, but then he reached up his hands slowly and applied a slight pressure to Eyepatch's stomach.

Eyepatch fell away from him easily, landing with a thud on the dusty concrete as its kagune receded into its back.

'They're eating me. They're eating me. This feeling… dissolving into their mouths…'

Eyepatch was lying defeatedly on the ground in front of him, but Amon knew its mind was somewhere else. The ghoul was, truly, the most crazed and insane thing he had ever seen. It began twisting into itself on the ground, muttering all the while.

'Watching me from inside my stomach. Scuttling in my ear. What's 1000 minus 7? I don't know… please… mother, please. I'll be a good boy. I can't eat anymore. I want to be free. Please… please…'

Amon stared at Eyepatch as he saw sobs shudder through it. It wasn't the first time he had seen Eyepatch cry, but it still had him rooted to the spot.

Because it went against everything Amon had ever learnt. Everything he had ever experienced. Ghouls were ruthless killers, and yet here was one lying on the floor, crying and calling out for its mother. There was nothing touching the ghoul, no obvious wound or injury of any kind, and yet it was writhing as though its insides were on fire.

'Maybe it is hurt, and I just can't see it,' Amon said under his breath. They had both been trapped beneath falling rock, after all…

The space they were in went suddenly quiet. The ghoul had apparently passed out, clutching itself tightly in a ball. All Amon could really see now was its bare back that had been sprouting kagune limbs moments before.

Amon retreated as far away as he could in that small space, and after having another half-hearted pull at his quinque, he knelt down on the floor, crossed his arms over his chest, and tried to figure out what the hell he was supposed to do now.

Sorry if it's a bit shoddy in some places. Please review... I would love to know what you think and if I should continue this story. :) Other people have to love a bit of Amoneki as much as I do haha.