The world of Virtua Quest is one where many people shrug off reality, and instead spend their free time in the Nexus, a vast virtual universe. Sei, is a cheerful fellow who's been tapped by his friend, Hayami, into trying out the life of a hunter, one who collects data chips from the far-flung reaches of the Nexus and then sells them for cash. Sei, curious about the occupation, yet slightly intimidated by the dangers involved, reluctantly accepts after a bit of influence from Hayami, and the thought about the bike that they are trying to finish in time for the race in the real world. After completing the Hunters' test and a brief explanation from Hayami about the Hunter's License rankings-LoA, HighA, and ExA- Sei finds the server address for Curio City, and marks his way to the location.
Right after he had just arrived, a strange creature named "Bit" appears from his Hunter's Glove at a blaze of light and announces that he will be his navigator throughout the servers he visits. Sei is fine with this, now that Bit had explained his startling entrance, but not with the fighters that pursued him a few minutes afterwards. Then a girl with aqua-colored hair approaches him and directs him to logout. Sei demands Bit to logout, but the command is not accessible. The girl then tells him to go to a warehouse and find what he needs there, and tells him that he's "in this fight,no matter what.
The only person that can defend you is yourself." Sei obeys, and heads to the warehouse, whereas falling through the glass ceiling. He meets a man that bears a vague resemblance to his father, and tells him that he may need to fight, questioning whether he considers to fight for himself or for others. Sei answers a baffled reply to this, and as to rid his anxiety, the man teaches him Sypnapse Break, a special technique bared by Hunters. Once taught this, Sei is confident, and starts his Hunter journey.
While looking around, Bit starts warning that there is a Virtua Soul in the area. Giving him a baffled look, Sei bursts a container and finds this strange cluster of data. "Is this...a Virtua Soul?" he reassures, and begins processing the data in his mind. Meeting a man named Akira that urges him to fight and "forge his path", Sei's attempts are futile, for Akira seems to read Sei's every move. But, he is taught his first Virtua Soul move at least. He wakes up and spots another fighting dummy abduct two Hunters through a window. Sei destroys the window and pursues after them, being sidetracked by more fighting dummies and two more Virtua Souls, as well as an enigma he spots in an elevator that smirks at him.
At the top of the elegant and abandoned building, he meets across a blonde African American in a load of armor. Despite his buff appearance, Sei easily defeated the "root user" as referred by the blue-haired girl, granting him the opportunity to logout, as well as the other hunters.
Back at the Hunter's place, Sei finds Hayami, and asks him about Virtua Souls. Hayami tells him that they are like "ghost data", meaning that they're to the point that they don't exist. Finding this useless, he asks the shopkeeper, and when her explanation isn't any help, he asks a man talking to a woman, and finally he reveals information: A man was rousing him for Virtua Souls, and he vanished in the Wild Corridor, yet another lost Server. Sei gains the server address to the Wild Corridor, and he too vanishes in the location.