Mamoru and Asahina are Ayato's classmates at the beginning of the anime, more so, they are very close friends. A big secret in shrowded in mystery concerning the identity of these two which isn't revealed until late in the series. Though Mamoru and Asahina share a relationship, it is apparent that Asahina also have deep feelings for Ayato. In fact, she's had feelings for Ayato for a long time, around the same time 14 year old Ayato and Haruka got together as a couple. Asahina stayed away from Ayato out of respect for his relationship with Haruka and eventually decided to get together with Mamoru, though unfortunately no deep feelings were shared for Mamoru like she had for Ayato.
Later in the series we find out that Mamoru and Asahina are being controlled/manipulated by Mulians. Though Mamoru accepted his identity as a Mulian and even started to work under the supervision of Maya, Asahina had a harder time coping with this discovery. At the beginning of the series Asahina actually has red blood, but during this time she wasn't controlled by a Mulian, so her blood hasn't turned blue yet. When Asahina discovered that her blood turned blue, she suffered an emotional breakdown and became very unstable. She decided to go with Ayato and get out of Tokyo Jupiter to see if she can find some truth, much to the disdain of Mamoru who then developed deep hatred for Ayato for what happened later.
On their time together, Ayato and Asahina had some very intimate moments (even romantic) but it all came to a startling stop when Asahina was finally turned into a dolem in episode 19, something she was trying to avoid. This is a very key episode in the series as it shows the transitions of what is seemingly a regular person who is then turned into a controlled host for a Mulian. All throughout this episode, Asahina was dying to tell Ayato that she may not be who she think she is... that she's not the Asahina Ayato once knew. Along with this secret Asahina wanted to confess her feelings for Ayato but evidently never got a chance to say it. When Asahina was taken over by the Mulian identity that has been haunting her in her mind through the Dolem, she suffered a physically and emotionally painful death as she was beaten to death by the clueless Ayato on the RahXephon; quite possibly one of the most tragic and beautifully executed death scenes in anime. At the end of this battle, Asahina left her confession of love to Ayato in writing.
When Mamoru finds out that Ayato killed Asahina (Ayato of course had no clue when he did it), he declares all-out revenge againts Ayato. Mamoru even comes out of Tokyo Jupiter and settles down in Ayato's place only to setup a fight with him later with his Dolem. Mamoru was killed by RahXephon-Ayato. At the end of the series though, after the tuning of the world we get to see part of a picture of Mamoru and Asahina who are in wedding garments. Next to the picture is an invitation for Ayato to a class reunion from Mamoru and Asahina Torigai.