The series revolves around Trojan as he gathers villains from the Original Machinima Universe such as: Beavis from (Chain)SAW, Yeti from The Hunt for Revenge, Piggsy from the unreleased Manhunt machinima, Ben Ross from Black Hydra, Zardon from The Rise of Demons, and Corona and Freddy Kreuger from the original Nintendo World series.
Trojan concludes that Tyler Redick, the writer of all the series, is the real threat as he is the one who writes the villain's deaths. Trojan then has every character return to their YouTube video and kill the hero, regardless of what the script says. Redick finds out when his YouTube account gets hate mail from aggravated fans. Trojan confronts Redick and tells him that they will come after him as soon as they find a way into the real world.
In response to this, Redick creates a virtual manifestation of JackSpicer2311, his YouTube account, and sends it into YouTube to battle the Evil Alliance. Jack kills Freddy and then recruits all of the side characters from the machinima so that they can band together to avenge the fallen heroes.
Redick cancelled the series after only two episodes because he did not know how to make the show last. According to Redick, the series was originally meant to be a short film, but fans requested it become a series. With no ideas on how to accomplish that, Redick cancelled the series.
With the creation of the New Machinima Universe in 2014, fans questioned if a remake of The Evil Alliance would be created. Redick commented "It's possible, but I need to expand the new Universe a little more before attempting a major cross-over."