One of the players, Kazuto "Kirito" Kirigaya, is one of 1,000 testers in the game's previous closed beta. With the advantage of previous VR gaming experience and a drive to protect other beta testers from discrimination, he isolates himself from the greater group and plays the game alone, bearing the mantle of "beater", or "beta tester" and "cheater". As the players progress through the game Kirito eventually befriends a young girl named Asuna Yūki, forming a relationship with and later marrying her in-game. After the duo discover the identity of Kayaba's secret ID Heathcliff in SAO, who was playing as the leader of the guild Asuna joined in, they confront and destroy him, freeing themselves and the other players from the game.

In the real world, Kazuto discovers that 300 SAO players, including Asuna, remain trapped in their NerveGear. As he goes to the hospital to see Asuna, he meets Shouzou Yūki, Asuna's father, who is asked by an associate of his, Nobuyuki Sugou to make a decision, which Sugou later reveals to be his marriage with Asuna, angering Kazuto. Several months later, he is informed by Agil, another SAO survivor, that a figure similar to Asuna was spotted on a giant tree (known as "The World Tree") in another VRMMORPG cyberspace called Alfheim Online (ALO). Assisted in-game by his cousin Suguha "Leafa" Kirigaya and Yui, a navigation pixie, he quickly learns that the trapped players in ALO are part of an evil plan conceived by Sugōu to perform illegal experiments on their minds. The ultimate goal is to perfect mind-control for financial gain and to subjugate Asuna, whom he intends to marry in the real world, to assume control of her family's corporation. Kirito eventually stops the experiment and rescues the remaining 300 SAO players, foiling Sugōu's plans. Before leaving ALO to see Asuna, Kayaba, who has uploaded his mind to the Internet using an experimental and destructively high-power version of NerveGear at the cost of his life, entrusts Kirito with The Seed – a package program designed to create virtual worlds. Kazuto eventually reunites with Asuna in the real world and The Seed is released onto the Internet, reviving the VRMMORPG industry.

Soon after, at the prompting of a government official investigating strange occurrences in VR, Kazuto takes on a job to investigate a series of murders involving another VRMMORPG called Gun Gale Online (GGO), the AmuSphere (the successor of the NerveGear), and a player called Death Gun. Aided by a female player named Shino "Sinon" Asada, he participates in a gunfight tournament called the Bullet of Bullets (BoB) and discovers the truth behind the murders, which originated with a player who participated in player-killing in SAO. Through his and Sinon's efforts, two suspects are captured, though the third suspect, Johnny Black, escapes.

Kazuto is later recruited to assist in testing an experimental FullDive machine, Soul Translator (STL), which has an interface that is far more realistic and complex than the previous machine he had played to help develop an artificial intelligence for the Ministry of Defense (MOD) named A.L.I.C.E. He tests the STL by entering a Virtual Reality cyberspace created with The Seed package, named UnderWorld (UW). In the UW, the flow of time proceeds a thousand times faster than in the real world, and Kirito's memories of what happens inside are restricted. However, Black critically injures Kazuto with suxamethonium chloride but the MOD recovers Kazuto and places him back into the STL to preserve his mind while attempts are made to save him.