Evil Energy is the name Duo gave to a type of energy that was brought to Earth accidentally during the Wily Wars when an Ancient android Duo was pursuing and battling crash landed on Shinigami Island. The remains of the robot, as well as the living energy mass inside, was studied and used by Dr. Wily as a kind of power source for his robots (such as Bass), noting that applications of Evil Energy caused an increase in power to robots.
Duo stated that exposure to evil thoughts such as those within Wily would cause the Evil Energy to spread, until it infected every living thing around. Evil Energy was poisonous to most Robot Masters, and nearly killed Rock, though a combination of Duo's ability to destroy Evil Energy and Rock's strong sense of justice and ethics (referred to by Duo as Justice Energy) helped save the Robot Master's life. Duo's mission on Earth was to destroy every last trace of Evil Energy to prevent its spread. Duo appears to have fulfilled his mission, left the planet, and has not been heard from since.
Curiously, Bass still contained Evil Energy even after the battle with Wily, and Duo did not act to try to remove it from Bass. Duo stated that Bass, too, had "Justice Energy", a fact that Bass patently denied (much to Duo's amusement).
The behavior of Evil Energy corresponds to that of Negative Energy, though in a sentient or semi-sentient form.