The Varia (as they are apparently called) are the villainous force from Syvalion. This mysterious alien race is plotting an invasion to Earth, abducting humans to be converted into robotic slaves. They are mutants with no shape of their own, being able to manifest out of thin air and possess human bodies.
Since the story of the game is played in a non-linear scenario system, every time the game is reset, rebooted or played the story is played differently at random, always revealing a small portion of the general plot. In most scenarios the unnamed hero (the story is told from the perspective of the unnamed hero in the form of diary entries) steals the Syvalion ship from the aliens to fight them. As it turns out, they were actually humans who were bio-engineered by scientists, but ended up being forgotten on another planet, where they evolved and plotted their revenge. In one of the scenarios, the hero meets with a pale old scientist, who was apparently one of their creators, trying to create a super intelligent being.
In most endings (the game is said to have 101 different endings, an unprecedented record) the hero thwarts the alien's schemes, but in some he fails to stop the invasion or is killed by them. While the hero's fate is unknown, the Syvalion ship have been somehow stolen by the Belser, who later converted it into the Dark Helios battleship. Endings are chosen randomly every time.
- Gigat - An arachnid-styled boss Varia.
- Armax - A bipedal, hopping boss Varia.
- Zandic - A plesiosaur-like boss Varia.
- Glodloid - An ammonite-like boss Varia.
- Keplos - A pterodactyl-like Varia boss.
- Xyzolog - A boss Varia looks like a sea urchin.
- Gattnoizer - A Cyclops boss Varia throwing sets of boomerangs.
- Megavalion - A second-generation robotic dragon made after Syvalion. Much more aggressive and powerful than its predecessor.
- Galdvalion - An upgraded version of Megavalion, with only 25% chance of appearing in the game. When it does show up, it always appears as the final boss of the game. Players' game skills better be excellent to meet this tough lad.
- Galst - Indestructible Varias that will step in to end Syvalion when the dragon dallies around instead of advancing, or time limits expires to zero. Syvalion may keep this creature at bay for a while, but eventually more Galsts will appear and overwhelm Syvalion.
- Although Syvalion is originally intended to have 104 different endings, 104th ending never materialized and endings 43th and 44th do not work due to bugs in the game.