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The Nanite Gods series was a fanfiction series that takes place after the series ends and was centered around the actions of Van Kleiss following his disappearance, causing the Second Nanite Event caused chaos to awaken around the world as four Meta-Nanites reprogram themselves and launch themselves around the world to pick new wielders while leaving the last with Rex, meanwhile a Sixth Meta-Nanite is found and is recognized as the strongest with the Code name "King".
The story begins the potential report of Providence being disbanded after there was a world-wide cure and the start of a normal day for Rex, however he soon falls down in agony as four colored lights burst from his chest and head off in different directions, the Meta-Nanites. Reports reach Providence of a second Nanite Event that has released highly unstable Nanites around the world and thus creating even more Evos. Van Kleiss' new plan, however, requires that he get into the Pentagon.
- Nathan Kleiss - Nathan Kleiss is the bearer of the long-lost "King" Meta-Nanite and an extremely powerful Human E.V.O that is described to be "Immortal" by his father: Van Kleiss, Nathan has a past with Rex and it was hinted that their relationship has always drawn them back together again and again despite the obstacles that appear before them.
- Rex Salazar - Bearer of one of the five normal Meta-Nanites and once bearer of all five normal Meta-Nanites, Rex lost four of the Meta-Nanites when Van Kleiss caused the Second Nanite Event and thus caused a new E.V.O War, Rex must join together with Nathan to combat the new E.V.O threat and gather the other Meta-Nanite bearers before something bad happens.