A/N: This story will focus mainly on AkihikoxShinjiro, but there are mentions of onesided MitsuruxAkihiko, onesided MinatoxAkihiko, implied FuukaxJunpei, and JunpeixChidori.
This is also more character introspection than actual plot, and was written over a year before it was posted (so, in mid-2013), but I'm proud of it, so here it is. Each chapter will be in the viewpoint of a different SEES member, and the chapters go in order of latest to earliest events time-wise.
I did take some liberties with headcanons, particularly with post-game events (which will be noticeable in this chapter especially), and this was written before I had played either Arena game, Persona Q, P3P, nor had any of the P3 movies come out. This is based solely on my interpretation of the characters in P3:FES.

It was years before Ken even considered what it was that made Akihiko so set on solitude. Sure, he had Ken and everybody who worked with him, and he even had Koromaru. Junpei visited often, and sometimes he even brought Fuuka along, who always insisted on cooking them all dinner. Thankfully, her cooking skills had improved since her high school years. Mitsuru called at least once a week, and visited once a year, whenever her career gave her the chance to return—however briefly—to Iwatodai.

Ken knew that it was his own doing, Akihiko living in Iwatodai. If it had been up to the man, he'd be traveling the world right now, refusing to think of the city of his childhood and all of the memories haunting it, but Ken had needed guidance and Akihiko had needed somewhere to call home, so they had both been drawn back to the place where it all began. After all, Ken still needed to make it through high school before Akihiko would so much as think about letting him travel the world.

The younger man had always assumed Akihiko avoiding the dating scene had been a choice made for Ken's own benefit. It would be harder to focus on his studies if his guardian was dragging random women into the house at all hours of the night, and even with a steady relationship, Ken would most likely then be expected to interact with the woman, and that would take away from his schoolwork as well. It took time before Ken fully realized how narrow this view of the world was and forced himself to look around.

Akihiko's decorating style was much to be desired, with any sort of "unnecessary" furniture-like paintings or decorative candles or flowers-virtually nonexistent. Not one portrait hung in the house. Not even Ken's school pictures. Not even the picture Akihiko had taken of himself with Mitsuru on the day of their graduation. Not even the group picture of all but one of the old members of SEES.

There was one picture that Akihiko kept standing safely on the table beside his bed. Though the door to his room was normally closed, the very few times it had been cracked, Ken had peered in out of curiosity and seen it, clear as day: A photo of Akihiko with Shinjiro, most likely taken before they had met Mitsuru, before they had formed SEES. The two of them looked happier than Ken had ever witnessed, arms thrown over each other's shoulders and grins stretching across their faces.

Even when he had seen the two of them smile in person, it had never looked quite like that. Shinjiro's rare smiles were small and never reached his eyes, and while Akihiko's were kinder, they were certainly not happier. The picture though seemed to have been snapped in a moment of ignorance between the two boys. For all Ken could tell, neither had any knowledge of the photographer until the flash had already gone off, and the image saved forever on a tiny square of film. Ken could tell by the look in their eyes that those smiles were meant for nobody but the one sitting beside them.

In all the time he had been staying with Akihiko, Ken had been shouted at only once. It happened to be the moment he walked into Akihiko's room with a question only to be greeted by the sight of his guardian sitting, silent tears running down his face, with that picture cradled in his lap.

And that was how Ken knew.