During the Xanatos crisis, a series of thefts occurred within the Jedi Temple, prompting the Jedi High Council to task Jedi Masters Qui-Gon Jinn and Tahl with identifying the perpetrator and bringing them before the council for judgment.
Once assigned to the task of finding the individual responsible, Master Jinn started to create a list detailing the items that had gone missing. Initially, the items seemed to be random and insignificant: a tool box, holo-files containing student information with names ranging from A to H, a teacher's robe, and a sports activity set. Tahl began investigating the missing records, interviewing the two volunteers that assisted Curator of Records T'un. Just as their investigation reached a standstill, the thief struck once more. From the training room used by the senior apprentices, all of the lightsabers were stolen. This resulted in all of the older Padawans being without their sabers, making them less effective in the event of an attack. Amidst the damaged tunics and debris, the two Jedi discovered a message written in red paint on the wall: COME, YOUR TIME WILL. BEWARE YOU MUST, TROUBLE I AM.
In response, the decision was made to notify the entire Temple about the intrusion, leading to a complete lockdown of the complex. All apprentices were required to obtain permission before leaving the Temple or using any facilities outside of their scheduled classes. Security inspections and interviews were conducted. Rumors began to circulate that the intruder had been sighted within the Temple. Jinn came to the conclusion that the Temple's security was flawed, as it heavily relied on the assumption that no Jedi would permit an intruder to enter, with minimal internal security measures. Emergency Code Fourteen was broadcasted over the intercom system, summoning the investigating Jedi to a small conference room where they met with Yoda. He informed them that the Healing Crystals of Fire had been stolen from their holding room, a deeply disturbing crime.
Following the break-in into Qui-Gon's quarters, the two Jedi compiled a list of two hundred and sixty-seven Jedi and non-Jedi staff who lacked solid alibis. After realizing that a scent Tahl had detected in Jinn's quarters matched the water from the lake level, Jinn and Bant Eerin dove into the depths of the lake to locate the stolen items. Upon discovering the lightsabers and other less important items inside a waterproof container, Jinn decided to use the container as bait; the perfect solution seemed to be leaving it submerged and waiting for the thief to return.
The two Jedi waited on the lake's edge; the lights were turned off because no one was authorized to enter any room except for scheduled classes. When someone finally arrived, Jinn discovered it was Bruck Chun, one of the numerous students they had questioned. Jinn followed him quietly, but his plan was disrupted when Tahl's droid, a 2JTJ personal navigation droid, started talking. Initiate Chun, startled, fled, but the mission was not a total loss; Tahl had noticed a figure following Jinn; despite knowing he did not reside at the Temple, the figure appeared familiar with the surroundings.
When Obi-Wan Kenobi, who had left the Order, requested Jinn's assistance on Melida/Daan, the Jedi quickly went to help him. While they were away, Yoda went to meditate in the Room of a Thousand Fountains early in the morning. Upon entering, he began to walk towards a small bridge, as was his custom. However, before crossing, he paused, just as the bridge exploded.
Jinn and Kenobi returned to find the Temple extremely hot, and some sections without power. Tech worker Miro Daroon was struggling to keep everything operational; each time he repaired something, he discovered another problem. After an unusually cold meeting with the Council, Kenobi, who was no longer a Jedi, went to the Lake Level with Bant. As they walked, a turbolift car, which was obscured by the bright lights above, was heard to be stuck. As the lights below it disappeared, the two friends were horrified to see that the car had derailed from its shaft and the lives of several initiates were now in danger. While Initiate Eerin summoned the Council, Kenobi entered the shaft via catwalk and assisted Ali-Alann in evacuating the clan. Once they were safely on the ground, the Masters, who had been using the Force to help support the unstable car, again scolded Kenobi for his recklessness and for almost putting the Initiates in unnecessary danger.
Following the incident, Daroon discovered that the car had clearly been sabotaged. Yoda decided it was time to reveal that the Jedi had accepted a mission from the Galactic Senate; they were safeguarding a large shipment of vertex in the Temple Treasury Room.
As Jinn made his way to the Temple tech center, he sensed a strong dark side presence in the Room of a Thousand Fountains. As the sabotage worsened, Daroon determined that it was necessary to shut down two sections of the Temple. He and Qui-Gon Jinn reviewed the Temple blueprints and concluded that the only solution was to shut down all the Temple systems and then restart them—a solution Jedi Daroon was hesitant to implement, as it would leave the Temple vulnerable.
After determining that Xanatos, Jinn's former Padawan, was involved, both Jedi concluded that watch teams needed to be stationed at all service tunnels that could be used by the Dark Jedi. However, it was Eerin who noticed the connection between the attacks and water. The water was pumped through interconnected pipes, and the pipes from the Lake Level were located near the tech center. Jinn enlisted Kenobi's help and they continued their mission to stop Xanatos. Daroon then planned to shut down all systems for twelve minutes. Eerin then led the other two down into the Temple's water purification levels. The tunnels would flood with water every twenty minutes before draining again. As the trio descended into the tunnel, they found a service tunnel and followed it until they were suspended on a catwalk above the water purification unit. It was there that Xanatos revealed himself, engaging Jinn and Kenobi in a brief duel before diving into the rushing water. When the Jedi realized that Tahl's droid had been reprogrammed to send information to Xanatos, Jinn asked Ali-Alann and Padawan Garen Muln to disguise themselves as him and Obi-Wan, respectively. As they prepared their plans, Jinn's comlink beeped, and when he answered, Xanatos spoke from the other end. The Dark Jedi had captured Eerin and was using her as bait by placing her underwater, where she would eventually drown.
As the Temple powered down, Jinn and Kenobi waited in the treasury room, where Chun and Xanatos were certain to appear. When they did, they began to duel; Kenobi would leave and follow Chun, who had been ordered to kill Eerin. Jinn and Xanatos' duel continued into the High Council Chambers where Xanatos shattered the window and jumped out.
Meanwhile, Kenobi chased Chun down the stairs that ran alongside the High Council turbolift shaft. Eventually, they arrived in the Room of a Thousand Fountains, where Kenobi believed Eerin was being held hostage. Because of the power outage, the large waterfalls had stopped flowing, but the water had not drained from the pool, and Kenobi noticed the different shade of blue in the water; Eerin's tunic. She was chained to the floor below, and Chun was trying to conceal this fact. When Chun taunted Kenobi about the death of his friend Cerasi on Melida/Daan, the young Jedi intensified his attack, forcing Chun up the rocky hill that formed the back of the waterfall. At the top, the Padawans fought for their lives. When Kenobi released his anger, he noticed that the lights had come back on. The water systems would follow. At that moment, the falls roared back to life; Chun lost his footing on the slippery moss in the waterfall bed and was swept over the edge. Kenobi tried to help but was too late; he saw Chun hit several rocks before his body landed on the grass, his neck twisted at an unnatural angle. After saving Eerin, he hurried to assist Jinn.
Jinn and Xanatos continued their duel on the Meditation Station outside the Council Room. The Jedi would later learn that Xanatos had rigged the Temple fusion furnace to explode when Daroon restarted the air circulation system; this was only discovered due to Xanatos' arrogance in revealing his plans. Kenobi met up with his master, who had allowed Xanatos to escape in order to save the Temple. They raced down through a food transport tube until they reached the Tech Room. Daroon directed Jinn to the reactor core of the furnace, where Jinn retrieved the Healing Crystals of Fire, which were the key to destroying the Temple. With that key removed, the crisis was over.