Haruka is shown to have very strong feelings for Ayato and struggles at maintaining a relationship with him for many reasons. Her position within TERRA makes Ayato think that she is only using him because of his ability to pilot the RahXephon. Ayato's own personal struggles also create barriers for their relationship.
SpoilerIt is later revealed that the girl that Ayato is constantly drawing and painting is actually a young Haruka. They had fallen in love when they were younger. The earliest date when the show places them together is at August 10, 2011, at age 13. When the Tokyo Jupiter barrier was established (just after the end of 2012), Haruka was on a vacation in a different part of Japan. Ixtli uses Ayato's distorted memories of Haruka to create the form of Reika Mishima. Haruka aged much more than Ayato in the outside world due to Tokyo Jupiter's time dilation effect. She had a relationship with Itsuki Kisaragi, possibly due to his similarity to Ayato.