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KOS-MOS has significant powers believed to be superior to all other party members. In addition to superhuman strength and speed, her body is formed from some sort of highly advanced nanomachines that allows her to morph parts of her body (specifically her arms) into various energy projectile and melee weapons. Her body is also able to self-repair and is very durable though not indestructible, and she is also protected by a force-shield. She also possesses the ability to summon weapons such as the F-GSHOT chainguns and her famous F-SCYTHE and equipment from another location via U.M.N. transport. She also has a long-range sensory array, the D.S.S.S. system and CPU that exceeds even those possessed by Observational Realians.She also possesses a Hilbert Effect projector whose power is thousands of times greater than that achieved by even the largest spaceships.
KOS-MOS possesses several black box components left behind by Kevin Winnicot. Each of these black box features are found in each of her skeletons, version 1, version 2, version 3, and version 4. One of these "black boxes" is her potent X-BUSTER weapon, a powerful burst of energy beams from her abdomen that absorb the Gnosis. Other black box components are related to her "simulated personality" OS and her self-awareness which is more in fact Mary Magdalene resting inside of her. KOS-MOS also has some form of energy manipulation tied to the Zohar. The Red Testament, Kevin Winnicot, claimed that KOS-MOS's power came from "U-DO using the Zohar as a door".
KOS-MOS has another weapon system called the Tertiary Weapon System, which is seen periodically throughout the series. They consist of a set of energy wings, a pair of energy cannons and other attachments meant to be fitted onto her. The wings and cannons are part of a Phase Transference Cannon. While wearing this gear she is shown in a premonition flying through space at sub-light speed and then confronting U-DO above an unknown planet. The exchange that follows destroys several galaxies. The "Third Armament" as its also known makes a real-time appearance in Episode II on the Ω System. KOS-MOS uses this equipment to protect Shion and the party from U-DO. In Episode 3, KOS-MOS uses the tertiary weapon system to penetrate the barrier that surrounded Rennes-Les-Chateau in order to help the Elsa crew. The Tertiary Weapon System is really only compatible with her Version 2 and Version 3 skeletons.
While she is programmed to protect Vector personnel unconditionally, her highest priority is to protect Shion specifically. As seen early in Episode I, she has the capacity to ignore Shion's orders if Kevin Winnicot (the Red Testament)'s pre-programmed directives supersede them. In Episode III, shortly after KOS-MOS is destroyed by T-elos and subsequently rebuilt she rejects the direct commands of Kevin Winnicot. She is rebuilt with some of the Professor's Erde Kaiser technology, which makes her much more powerful than before.