At First Koutarou see's her in his dream, killing him in many ways.They saw each other in school at night where Koutarou saw Monsters.A small meteorite fell on Kagari's head which lead to amnesia. Kotarou takes care of Kagari and develops feelings for her.
After meeting her in the Moon Route, his love of Kagari gradually shifted to Moon Kagari instead. She also reciprocates his feelings, and both end up with each other at the end in the Terra Route on the moon.
Although Kotarou desires to be friends, Yoshino thinks the opposite and disagrees only seeing rivalry between the two. Behind all that, Yoshino actually looks up to him in a certain way. One attribute they both is share is they are loners, Yoshino at a higher degree, but they often have clashing ideas, so they are like opposites. Kotarou and Yoshino bicker and have quarrels often, and aren't reluctant to physically fight each other due to a former debate.
The two are actually close but it does not seem that way, with them both insulting each other and fighting for Chihaya's affections. Sakuya enjoys humiliating him with the nickname 'Fatarou kun'. Sometimes Kotarou sympathizes for Sakuya when Chihaya unintentionally upsets him with a comment with an agitated tone to it, then Sakuya turns solid stiff and paralyzed, frozen in shock. Kotarou uses Sakuya's phobia of cats to his benefit and makes fun of it, to Sakuya's displeasure.
The two of them are childhood friends, though the memories are hazy for Kotarou, because of the accident. After Kotarou's coma and his drastic change in personality, they get along suprisingly well, especially when they play around with their jokes. It should be noted that before they join Occult Research Club, Kotori is the only one Kotarou consider to be his friend.
It is revealed in the Terra Route that their relationship is nothing alike what it is in the Common Route. They practically despised each other, despite their similarities, though they sort of shared an older brother little sister bond.
Kotarou sees Kotori as a potential love interest, no matter how many times Kotori rejects him, he doesn't desist liking her. It is may not actually be unrequited love, it is likely she likes him as well. However, they avoid getting too close and thus, sometimes, there are awkward moments in their interactions when Kotori's trying to dodge Kotarou's feeling and Kotarou's lack of courage to approach her.
|“|| I'm like the Moon. A satellite passing the Earth, but never touching it...
–Kotarou, regarding their awkward relationship in Kotori's route
In Kotori's Harvest Festa route, Kotarou finally gather his guts to openly chase after Kotori while she keeps running away from him (both literally and figuratively). In the end, due to his previous injury, he collapses. Kotori comes back and makes him rest his head on her lap. He then proceeds to confess to her, which she happily accept after some time hesitating.
|“|| You, since long ago, stood on my road. I...was bad at being there. Many bad thing happened between us too...but, the truth is...I want to be accepted by you. I want to tell you.. that you are incredible. When you are hurt...I want to support you.
Those aren't half assed feeling at all. There is something else too. You may have thought my past self wasn't interested in you at all..But that's not true. Because I was shy, I couldn't say anything. When I was a kid too, I've always hated myself for being like that. I always wished to change, and the results are...
I love you, Kotori. I don't want to give you to any other guy. I want to cry with you. I want to hold you. That's why...would you want to be with me?
–Kotarou, his confession to Kotori
Lucia finds Kotarou a nuisance at the beginning, finding it necessary to make Kotarou compensate by giving him pain.
In her route, eventually, she resolves never to do that again. The two get along very well after the occured event in the chapel, where Kotarou vows never to leave Lucia's side.
Chihaya has a habit of saying "Thats what I hate about you!" Which at some point hurt Kotarou's feelings but he decides to hide this. At first, Chihaya tends to have a tsundere like personality, but starts to warm up to Kotarou at a quicker rate than Lucia and Kotori.
Akane generally shows her other personality to Kotarou, which is not her myserious one. Akane has had a rough past, living in an orphanage specially for children with mental difficulties, so sometimes she needs someone to let out all her emotions to, which is Kotarou. Despite the fact she states she finds humans disgusting, Kotarou is an exception.
Kotarou finds it entertaining to tease and joke around with Shizuru, who does not realize his true intentions. Slowly they both begin to see each other in a more romantic view. At some point in her route, she reveals her past to Kotarou who sympathizes with her, and makes him love her more other than pity.