- "We had come so far, but we knew so little. And now, the true battle was about to begin..."
- — Kite —
.hack//MUTATION (.hack//悪性変異 Vol.2) (Japanese title: Malignant Mutation) is the second of the four-part video game series that is the core of the .hack franchise. It continues immediately after Infection and follows the heroes Kite and BlackRose as they become even more involved with what is hidden within The World.
The game comes packed with the second Liminality disc, "In the Case of Yuki Aihara." The instruction manual also came with two cut-out coupons: one for $5 off on the purchase of .hack//Infection and another for Outbreak. In Japan, a limited edition bust of BlackRose was given out to people who reserved Mutation. Because it was unpainted, it could also be a Mimiru bust.
Kite and BlackRose return to Θ Chosen Hopeless Nothingness but find part of the area locked off. After a quick intervention with Balmung, the two return to Dun Loireag, where Kite is told that his Book of Law he won from the Level Up Campaign has an error that prevents it from being installed, so it is replaced with the Book of Absolute (which also cannot be installed). BlackRose claims to have never heard of the event.
The two receive e-mails telling them to come to Θ Soaring Sky Bounded Abyss if they want to know more about the coma victims. It is actually a trap set up by system administrator Lios. Lios says that they should not pursue the matter any further and proceeds to delete Kite's character data along with the bracelet. Helba, however, interferes, saying that they cannot be deleted because of a mysterious encryption implanted in their character data. She introduces the theory that The World is based on the Epitaph of Twilight, telling the two to look to the Epitaph for clues. She then suggests to Lios to observe the two rather than try to delete them. Lios eventually agrees, deciding to use the two and the unique abilities of the bracelet to investigate the corrupted areas.
In one of the two areas Lios assigns the two to investigate, they meet with a vagrant AI named Sheraton, who gives them the keywords Λ Resurrecting Confused Judgement. Despite Lios's orders to not make any moves, they go to that area's dungeon and fight Innis. Kite Data Drains Innis and receives an item named "Segment 1." With Innis's defeat came another system crash, and the two are reprimanded once again by Lios.
Kite receives an e-mail from Aura with the keywords Λ Merciless Grieving Furnace. As Kite is about to enter, he meets up with Mistral and takes her with him. In the dungeon, he finally tells her about his unique situation. Although Mistral thinks he's merely role-playing, she realizes he is telling the truth when she sees Aura for the first time. Kite's Segment 1 returns to Aura's body, but he is immediately attacked by Cubia. Kite and Mistral successfully force Cubia to retreat. After the battle, Mistral acknowledges Kite's plight and promises to do all she can to help.
Kite continues to search for clues relating to Epitaph of Twilight, and learns from the BBS that a player named Wiseman specializes in such info. At Λ Dying Madness Haunted Land, Wiseman says that the info is not cheap, and says he will trade the info but he will think of the conditions first. He sends an e-mail telling Kite that he will trade for the Spark Sword located at Λ Blooming Promised Walkway. The area is a protected one, but Kite needs as much information as possible, so he gate hacks inside and retrieves the sword after Data Draining a Dalaigon Data Bug. Kite trades the sword, but Wiseman demands to know how he managed to get the sword from a protected area. After listening to Kite's story, he agrees to send an e-mail containing all the data he has and returns the Spark Sword, saying that the story was far more interesting than the item.
Wiseman's e-mail contains an excerpt naming the eight Phases as well as a spell to enter Net Slum. The keywords are unknown, but there is a clue on the BBS. The keywords to the proper field are retrieved from an AI named Plaird. With the proper information and a virus core supplied by Balmung, Kite and BlackRose head to Λ Pulsating Worst Core. The two find their way to Net Slum, an area where damaged data is gathered. Helba meets them there, as does Balmung, who followed Kite and BlackRose to Net Slum. Balmung claims that his shady tactics were all for preserving the order of The World. Lios also appears and threatens to delete Kite's party and the entirety of Net Slum, but before he can attempt it, the third Phase, Magus, appears in front of Kite's party. Due to power of the malicious program, Balmung and Lios are forced to retreat. Helba follows suit soon after.
Kite once again succeeds in Data Draining the challenging Phase, and he and BlackRose return to Λ Server. The two are shocked to find that the corruption they encountered in protected areas has now spread to The World's servers.
Characters Introduced in this Volume
- Λ Capricious Unending Corridor
Find Gemini Soul in a chest and Chinese Food from the Gott treasure.
- Λ Bottomless Soul Kaleidoscope
Password found on the back of .hack//SIGN DVD 2, Outcast. Receive BL Yokohama from the Gott Statue.
- Λ Lightless Sacred Remains
Password found on the back of .hack//SIGN DVD 3, Gestalt. Receive Bent Glasses from the Gott Statue.
- Early versions of the cover shown on several .hack official websites differ from the final cover for all regions in that the background for the flying debris is green, not red-orange, and the position of Kite's eyes also change between the two versions.
- This is the first .hack game to feature SIGN characters.
- All the promotional items for Mutation are allusions to its included Liminality DVD.