Apparently you didn't try to understand the events of the series
. Haruko does not have a "thing" for Naota. She is only using him for his head and N.O Channel to get to Atomsk, as he is able to channel Atomsk's power when he is with Canti (she wanted to use the N.O Channel to get Atomsk out of Medical Mechanica and merge with him, but did not realize that he was already "out"). Nothing more. Her only real focus is getting rid of Medical Mechanica and getting Atomsk's power. She is only messing with Naota's head. The more emotional Naota gets, the more likely that something will come out of Naota's head, as his mind is "unstable" because he tries to be an adult. And Naota only felt uncomfortable around Haruko when he didn't understand what she was doing. After she came back from her "vacation", he realized his feelings for her, although the feeling was not mutual.
And the thing with Naota's father? She did not do anything sexual to him. In the fourth episode, Kamon was actually "dead" for the majority of the episode. Before the events of the fourth episode started, Haruko tried to use Kamon's head as an N.O Channel. He happily agreed to do it, as he has a big crush on her. However, not only did his head not work, the hit he received from Haruko "killed" him. So the Kamon you see throughout the episode, even in the sex scenes (which might not have been sex), is actually a robot ("Robo-Kamon") that Haruko built to hide what she did and to get on Naota's nerves. Naota is not cooperating with Haruko, so Haruko hopes that when Naota sees her "fooling around" with his "father", he will become jealous and be more willing to work with her. Naota eventually finds his "dead" father (after destroying Robo-Kamon) and revives him with water.
Anything else you don't understand?
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