Commander Amarao (指揮官・アマラオ?, Shiki-kan Amarao) is a special agent of the Bureau of Interstellar Immigration who, apparently, has some past history with Haruko and claims to "know who or what" she really is. Amarao's childhood seems to mirror Naota's.
Commander Amarao works for the Bureau of Interstellar Immigration. This agency, among other things, acts as a middle man for negotiations between the government and Medical Mechanica. Thus, Haruko is a big problem for them as she is bent on provoking an attack by disrupting communications. It is a likely inference from FLCL's story that as a child, he was approached by Haruko, just like Naota, and she tried using his N.O. to capture Atomsk. However, his N.O. channel is so weak that he can barely pull through something the size of a slingshot (actually a small guitar and used as intended). Despite not appearing in FLCL Progressive, Masurao, a man who also has red hair, is pointed out as his son due to their shared small eyebrows trait. This is later confirmed in the final episode.
Amarao first appears in the fourth episode of the series, giving viewers the impression that he is virtually an omniscient character as he gives background information as well as making fairly accurate predictions. However, subsequent events would show him as extremely weak and very limited in foresight, though he seems to grasp what is happening better than almost all the other characters. He has a love for sickeningly sweet candy and drinks (which he claims will help bring people's brains back to normal), and hates spicy, sour, and pulpy foods — much like Naota.
Amarao wears fake eyebrows made of nori, which he believes serve the dual purpose of protecting him from N.O. and making him look tough. He has blue eyes and red hair, though his trip to the hair salon in episode 5 suggests that this may not be its natural color. He always wears a black suit and tie, often paired with a green trench coat and sunglasses with yellow lenses.
Amarao's vehicle of choice is a Fuji Rabbit, a motor scooter which was initially produced in 1946, six months prior to the initial production of the Vespa. Given that throughout the series, Amarao is constantly trying to impress Haruko, who rides a Vespa, one could conclude his ownership of a scooter is a further manifestation of his attempts to impress her — or, at the very least, a signal to the level at which Haruko had influenced him in his youth.
From their very first meeting, Amarao is constantly warning Naota about how dangerous Haruko is, and is thus trying to keep Naota from ending up like he did because of her. Amarao knows many details about Naota's life, too, meaning that Amarao had been watching him closely for some time. Naota has a much stronger N.O. channel connection than Amarao does, so Haruko actually finds him more useful to her than him. This and some other signs suggest that Amarao feels jealousy that Haruko chose Naota over him.
Judging by the way Amarao acts around Haruko or while talking about her, he probably has some feelings for her. However, she is a troublesome alien, so those feelings are diluted by his anger towards her for what she did to him, and the trouble she causes. He always calls her "Raharu," believing that is her real name. It is just as likely that that is simply another false alias, however. Haruko finds Amarao to be completely weak and pathetic for his weak N.O. channel, and doesn't fail to let him know.
Amarao never really interacts with the robot, but is aware of his connection to Medical Mechanica. He even seems to know about Canti's link to Atomsk before Haruko does. For these reasons, Amarao considers Canti to be a threat to the Earth's safety and tries to deal with him before MM or Haruko can use him for their own reasons.
Amarao's attractive young subordinate is often seen either giving out vital mission data, or on the field in investigations with Amarao. He hits on her in the final episode, but she resists him. In fact, Kitsurubami seems to be generally disgusted by the idea of romantic involvement with Amarao (and likely any form of physical contact), though she looks up to him as a superior and follows his orders loyally.
Although Amarao is the first to mention the Pirate King, his only information came from rumors and he had never seen him. In the final episode Amarao portrays Atomsk inaccurately, imagining Atomsk's appearance as a humanoid male figure with fiery red hair when he describes him to Naota. In an interview, the director clarifies that Atomsk's true form is indeed that of the bird, and Amarao's mental image was of a man because he believed that Atomsk and Haruko were lovers, which was later exposed to be false; Amarao looks very surprised when he sees Atomsk's true form. The director hinted that Amarao's misconception of Atomsk's form reflected his insecurity and jealousy, as he erroneously thought Atomsk was Haruko's boyfriend and therefore envisioned him as a masculine human male.