Nanites are microscopic robots created by Dr. Eggman at various times during his efforts to conquer Mobius. Programmed or controlled by an AI, they can restructure themselves into various forms and are thus extremely versatile. Most of the nanites were later taken over by NICOLE for benevolent purposes, including the construction of New Mobotropolis.
The earliest nanites created by Dr. Eggman were employed a weapons against the Secret Service, who were briefly captured and held in Robotropolis. Subsequently released, the members of the group were then debilitated by the infection while their reprogrammed robotic teammates Heavy and Bomb were ordered to eliminate the House of Acorn. The assassination plot was thwarted, and the Secret Service members underwent treatment to see the devices removed. Later, a far more advanced variety was created as a byproduct of Eggman creating Metal Sonic v3.0. (StH: #97, #102, #118, #146)
This new breed of nanites was later commandeered by A.D.A.M., and they became a serious menace to several groups of Freedom Fighters, including the Wolf Pack. A.D.A.M. spread them out and formed a city-like structure with them, eventually building a giant spire with which he planned to collect all the Chaos Emeralds in the universe by jump-starting the Great Harmony through the use of Turbo Tails and Super Shadow. Taking advantage of the nanites that infected the robotic components of NICOLE, Bunnie Rabbot, and Jules Hedgehog, as well as the inorganic shell of Tommy Turtle, he used them all as tools in his plan; however, when he was ultimately destroyed, NICOLE took control of the nanites, reshaping the nanite city into a recreation of the former Mobotropolis for her friends along with giving herself the power she needed to sustain her holographic form. (StH: #152, #168, #169, #176)
While initially a boon under NICOLE's control, the nanites would eventually turn out to be the Republic of Acorn's Achilles' heel when the Iron Queen used her Magitek powers to take over NICOLE and by extension the nanites, giving the Iron Dominion near-total control of the city. NICOLE (now rechristened Iron NICOLE) used the nanites to place the city under lockdown and form giant hands to capture any inhabitants that failed to comply with orders to surrender. (StH: #208)
After she had regained her free will, NICOLE used a portion of the nanites in order to create an underground bunker for Geoffrey St. John, Antoine D'Coolette, Bunnie, and Amy Rose. This bunker would later become Secret HQ, base of operations for the Secret Freedom Fighters. NICOLE and the Iron Queen also employed the nanites in battle against each other after Sonic, Sally, Monkey Khan, and Tails returned to the city from the Dragon Kingdom to face off with the queen. When her allies and minions were dispersed, the queen shaped the nanites into a robotic escape vehicle known as the Iron Dragon, only to have it be destroyed while she was attempting to leave the city. (StH: #209, #210, #211, #238, #240)
- It is possible that in the new timeline, the Nanites never existed on Mobius since New Mobotropolis is not made out of Nanite technology.