ATOMSK SPOILER!
Medical Mechanica has contained him. Haruko wants him badly enough to manipulate everyone around her for a chance to reach him. Amarao speaks about him with the nervousness of someone who understands that neither Haruko nor Medical Mechanica should be allowed to control that much power.
For most of the OVA Atomsk is less a conventional character than a presence moving behind Canti, Haruko and Naota. His mark appears when Canti draws on his power, and the full scale of what everyone has been chasing is not revealed until the climax.
When Atomsk finally manifests through Naota, Haruko's plan fails at the moment she seems closest to succeeding. Naota briefly becomes the vessel for the power she wanted, then releases Atomsk instead of handing that power to her.
The OVA never needs Atomsk to explain himself. Everyone else's reaction to him tells us why he matters.
ATOMSK THROUGH THE ARCHIVE //
ATOMSK & MEDICAL MECHANICA //
Open page →Who / What is Atomsk?
Open →The Pirate King · The Power Everyone Wants
For most of FLCL he exists through other characters rather than through explanation. His mark appears when Canti draws on extraordinary power. Amarao warns Naota about Haruko's pursuit of him. Haruko keeps forcing open N.O. routes because she believes they can lead her to him.
By the time Atomsk finally manifests, Naota has spent most of the series standing in the middle of a struggle he barely understood.
The Crimson Bird
Open →Atomsk's Final Manifestation
The image connects back to the red power associated with Canti whenever Naota is absorbed into him, but the OVA does not stop to provide a biological or technical explanation for Atomsk's form.
Atomsk's Bass Guitar
Open →Crimson Gibson EB-0 · Pulled Through Naota
The bass eventually becomes part of the final confrontation between Naota and Haruko.
Naota Is the Route · Atomsk Is the Target
It is not.
What she actually wants is Atomsk. Naota matters because his N.O. ability gives her an unusually powerful route through which objects, Medical Mechanica machines and eventually Atomsk himself can cross into Mabase.
That makes Haruko's relationship with Naota uncomfortable by design. She enjoys him, provokes him and becomes part of his life, but she is also using his body and his feelings to pursue something she wanted before she ever met him.