A Hildroid is a living organism developed by humans. As submissive as robots, they are used to carry out dangerous tasks instead of humans.
Several years later, a nuclear war breaks out for unknown causes. As a result of this war, several shifts in the earth's axis occur and the Hildroids, affected by the radiation, undergo major alterations. They become able to think and move with their own will and soon they start to kill their human hosts.
It's now several decades later and everything is normal at the space station for artificial hibernation testing. On board is Captain Waffle who has just woken from his frozen sleep.
Meanwhile back on earth, with the alterations in the earth's axis, animals and people appear from the past and become hosts to the Hildroid robots. The Hildroids begin to interfere with the histories of their hosts.
Captain Waffle, judging that the next shift in the earth's axis will cause major alterations in earth's history, descends to earth in a one-man escape ship. -Spinal Breakers
The Hildroid were originally docile beings created by humans as organic robots to perform dangerous tasks. However, radiation from a nuclear war made them become sentient, and they rebelled, attempting to destroy their human masters. Due to shifts in the Earth's axis, the Hildroid gain the ability to travel through time and begin to infect humans and animals in the Earth's past in order to alter human history. The infected beings are zombie-like, sometimes composed of assorted body parts, and they bleed green blood.
If the player chooses Captain Waffle ("The Man") in single player mode, Waffle and other Diabloon pilotss are shown destroying the enemy base. The game states that the Hildroid have been defeated, but that they will return in the future. Incidentally, in the similar ending featured in Sonic Wings Special, the enemy forces are not named.
It is not clear just which enemies are part of the Hildroid, as many of the game's bosses appeared in earlier and later games as part of Fata Morgana. It is possible that the Hildroid have joined forces with Fata Morgana. However, some enemies are marked with the same style of eyeballs found on the Eye Monster and Hildroid Monster, suggesting that those enemies are part of the Hildroid instead.