Trismegistus is the fourth and final episode of .hack//Liminality.
Several weeks after the meeting in Hida-Takayama on Christmas Eve Junichiro Tokuoka, Kyoko Tohno, Yuki Aihara, and Mai Minase all gather on a dinner boat in Tokyo Bay. Despite their nervousness, each one is dedicated to helping Ichiro Sato complete the mission sent from Helba. Ichiro himself soon arrives on a different boat. While traveling to their destination, Ichiro reveals the true nature of the problems that have been plaguing The World. Harald Hoerwick's program, Fragment, had in reality been nothing more than a program to create an "Ultimate AI". The system to create this A.I. had accidently become self-aware, and was trying to delay the birth of the A.I. to keep itself from finishing its purpose and ceasing to exist. If the problems are to be solved, the Ultimate A.I. must be born, and it's up to Tokuoka and his team to help that event occur.
Under the cover of nightfall they sneak into a CC Corp data station located on the edge of the bay. Avoiding the guards, Ichiro hacks into the security system allowing them to enter the main building. Inside the control room, Tokuoka begins setting up their hardware for hooking up to Helba's private server. Unfortunately the data has to compile, an act which will take about 15–20 minutes to complete. While he waits, Tokuoka asks Yuki to bring him some coffee from a vending machine. She gets the coffee and brings it to him, not realizing that she just created several new problems.
Outside, a patrol car comes by, investigating the entrance into the facility. They figure it's nothing more than a system error but realize somebody is actually inside when they discover that somebody used one of the vending machines inside. Realizing they have been discovered, Ichiro enlists the help of Yuki and Kyoko to buy Tokuoka and Mai some time.
The data now compiled Tokuoka logs into The World using Sieg's account. While Mai pilots the dummy character, Tokuoka watches the data streams. Mai finds herself watching a battle involving Sieg and a character named Orca (she is actually watching Kite and the .hackers fight against Corbenik). Suddenly, the server begins to malfunction and crash as CC Corp begins deleting their servers. Tokuoka realizes that if they complete this, everybody who is currently fighting will fall into a coma and the Ultimate A.I. will never be born. As he struggles to come up with a solution, Ichiro comes in and announces that they're out of time.
Outside the station Kyoko and Yuki find themselves being chased by guards, while inside Mai, Tokuoka, and Ichiro listen as other guards try to beat down the door to the control room. Tokuoka finally comes up with a last ditch plan, to transfer the entire battle onto a completely new server. Ichiro says that the plan could work, but that the timing would have to be exact. With no other options left Tokuoka puts his plan into action. Mai with her supersensitive hearing is put in charge of the timing, and manages to move the server right before it crashes, stabilizing the system and allowing the battle to continue.
Shortly after, the door to the control room opens and the Guards find themselves facing Ichiro. He calmly pulls out a business card and says that the entire thing was a test of their security system. With his fake credentials the guards have no choice but to believe him and are forced to let him go. Meanwhile, Tokuoka fights off against several of the guards allowing Mai and the other girls to escape onto the boat. Tokuoka is badly beaten and thrown in jail, but is released after Helba deletes all of the charges against him. Walking out of the police station, he finds Mai and the girls waiting for him. Mai says that they lost all their evidence, and Tokuoka pulls out a disk containing enough evidence to bring CC Corp to court. The four happily go out to eat and celebrate their victory.