It replaced the cancelled sequel Star Wars: Jedi Knight III: Brink of Darkness.
Jaden Korr and other students were traveling to Yavin 4 to begin their training at the Jedi Praxeum. As they were approaching their destination, their shuttle was damaged and had to make a crash-landing. Korr and Rosh Penin were separated from the group and had to navigate their way through the jungle. Along the way, they fought some howlers and encountered the Disciples of Ragnos, a Sith cult. Korr also saw the cultists using a scepter to drain Force energy from the Massassi temple. When the Jedi were finding the missing students, the Dark Jedi Alora broke into the personal room of Jedi Master Luke Skywalker and stole a record of places where Skywalker felt a strong connection to the Force. She gave it to her master, who was later revealed to be Tavion.
At the Jedi Academy, Skywalker assigned Jedi Master Kyle Katarn to teach Korr and Penin. After completing his basic training, Korr, as a Jedi Initiate, went on missions to Mos Eisley, Tatooine, Bakura, Blenjeel, and Corellia to investigate cult activities. During this time, he learned that the cult was working closely with the Imperial Remnant. After the five missions, Skywalker sent Korr to Hoth to investigate the site where he had a vision of Obi-Wan Kenobi. Although Korr did not sense any Force energy at the location, he discovered that the Imperial Remnant was also on Hoth. While exploring the ruins of Echo Base, Korr encountered Alora and dueled her before she escaped. Around the same time, Penin went missing during his mission to Byss.
Korr was promoted to Apprentice for his achievements on Hoth, and he progressed to the next stage of training. He completed another five missions to Nar Kreeta, Zonju V, Kril'Dor, Coruscant, and Dosuun. In the meantime, Skywalker discovered that the cultists had been draining Force energy from the locations mentioned in his record. He sent all available Jedi to investigate these places and directed them to travel in pairs—as a precaution after Penin's disappearance. Korr and Katarn were sent to check out Darth Vader's castle on Vjun. While exploring the castle, they destroyed a power generator to cut a path to the upper levels. However, the ensuing explosion separated Korr from Katarn. Korr moved on alone into the meditation chamber, where he encountered the Kothos twins and Penin, who had turned to the dark side. He killed the Kothos twins and dueled Penin until Katarn caught up and stopped them. At the same moment, Tavion showed up and used Force lightning to hold back Katarn and Korr before revealing herself as Penin's new master and the leader of the cult.She then took Jaden Korr's first lightsaber at the ceiling to collapse it and break the stalemate, Tavion then destroyed Jaden's lightsaber with the scepter and fled with Rosh. Kyle used the Force to temporarily hold up the ceiling while Korr cut a hole in the ground with Katarn's lightsaber, and the two of them jumped through the hole safely to the level below.
Upon returning to the Jedi Academy, Katarn and Korr reported their findings to Skywalker. For displaying courage and skill in defeating the Dark Jedi, Korr received a promotion to Jedi Knight, and constructed a new lightsaber. Katarn sensed Korr's anger at Penin's betrayal and warned him that his anger could lead him to the dark side. While Skywalker and Katarn tried to find out what Tavion intended to do with the scepter, Korr completed another five missions to Chandrila, Tanaab, Yalara, Byss, and Ord Mantell. After Korr finished the fifth mission, Skywalker gathered all the Jedi and told them that he suspected that the cultists wanted to use the Force energy stored in the scepter to resurrect Marka Ragnos, an ancient Sith Lord.
As the Jedi prepared to go to Korriban to stop the cult, Katarn told Korr that he had received a distress call from Penin, who said he was being held captive in an Imperial facility on Taspir III. When Korr raised concerns that Penin could still be with the dark side and was trying to lure them into a trap, Katarn told Korr that he would not abandon Penin even if it were a trap. Korr then reluctantly followed Katarn to Taspir III, where they split up at the facility to find Penin. Korr was the first to find Penin, who apologized to him and implored him to bring him back to the Jedi Academy. However, Korr turned furious because he thought that Penin had lured him into a trap, so he ignited his lightsaber and pointed it at Penin. While Alora tried to instigate Korr to kill Penin and join the dark side, Katarn used the Force to communicate telepathically with Korr and persuade him to spare Penin. Korr realized his mistake and let go of his anger; he kept his lightsaber and tried to leave with Penin. Alora attacked them and cut off Penin's arm. Korr then dueled Alora and eventually slew her. Katarn showed up and told Korr to leave for Korriban first; he would catch up later after bringing Penin to seek medical attention.
Korr landed on Korriban and joined the other Jedi in fighting the cultists while navigating his way through the Sith catacombs. He entered the Tomb of Marka Ragnos and saw Tavion using the scepter to transfer Force energy into the tomb. After Korr defeated Tavion in a lightsaber duel, Ragnos' spirit rose from the tomb and possessed Tavion. The possessed Tavion unsheathed a Sith sword hidden in the scepter and used it to fight Korr. Korr eventually defeated the possessed Tavion and destroyed the scepter with his lightsaber. Ragnos' spirit left Tavion's body and swore vengeance before returning to his tomb, leaving only a dead Tavion behind. After exiting the tomb, Jaden sealed the entrance and met Skywalker and Katarn on the way out, and they returned to the Jedi Academy together. In the meantime, New Republic Star Cruisers attacked and destroyed the Imperial Star Destroyer providing support to the cultists, ending the Battle of Korriban. Korr was honored as a valuable member of the Jedi Order and continued to go on missions to maintain peace in the galaxy. On the other hand, a redeemed Penin was accepted back into the Jedi Academy and got a prosthetic arm.
Korr can turn to the dark side by killing Penin in the Imperial facility on Taspir III. After igniting his lightsaber through Penin's body, Korr cast him aside and declared that he wanted the scepter and its power for himself. He then dueled Alora and killed her before leaving for Korriban. Katarn showed up too late and reassured a dying Penin that he was a Jedi; Penin died in peace. Katarn then rushed to Korriban to find Korr and stop him.
On Korriban, Korr attacked and killed everyone who stood in his way. He entered Ragnos' tomb and killed Tavion in a lightsaber duel. Just as he was about to take the scepter, Katarn showed up and urged him to resist the lure of the dark side and end the conflict. Korr refused and engaged his former master in a lightsaber duel. Toward the end of the duel, Korr used the Force to grab the scepter and blast Force energy at Katarn, knocking him out. He then used the scepter to make a pile of rocks fall on Katarn, and blasted a hole in the wall to make his way out of the tomb. A while later, Skywalker came in and saved Katarn, who told him that Korr had killed Penin and turned to the dark side. Skywalker said he could still sense good in Korr; Katarn left to find Korr in an attempt to turn him back. Meanwhile, Korr boarded the Imperial Star Destroyer, killed its commander, and seized command of the ship.
The game is powered by the Quake III Arena graphics engine, with modifications to give a third-person view and new lightsaber effects. Players now have the ability to construct their own lightsaber by choosing the hilt style and color. After completing certain objectives, new saber styles become available including the ability to wield dual lightsabers as used by Anakin Skywalker during the closing fight in Star Wars: Episode II Attack of the Clones (but first seen in Star Wars: Jedi Knight: Dark Forces II by the Dark Jedi Boc Aseca), or the double-bladed lightsaber made famous by Darth Maul in Star Wars: Episode I The Phantom Menace and first used by Exar Kun in Tales of the Jedi.
The main character of the game, Jaden Korr, was named Atton Rand in early drafts. The name was later used in Star Wars: Knights of the Old Republic II: The Sith Lords. One of Atton's in-game Easter egg lines is a joke about him being added to the game last minute, and how he was supposed to have been in "a spin-off to Jedi Knight."
Using a cheat code, players can have level 4 Mind trick (normally the highest level is 3). Using this, players can take direct control of an NPC. Other NPCs ignore the captured NPC; however, Jaden is susceptible to attack and players cannot fight back until the player regains control of Jaden by waiting until the Mind trick time limit expires, killing the NPC (this can be done by either throwing them off a cliff or shooting at Jaden if the player has saber defend on 3), or by pressing the Mind trick command key again which immediately cancels the level 4 Mind trick. Also, when using mind trick, the screen looks the same as when controlling a droid in Jedi Outcast. Controlling droids is also possible, as well as various NPCs, using a cheat code. Specifically, after enabling the cheats (by typing 'helpusobi 1' in the console), merely spawn an NPC with a name. (Example: "npc spawn stormtrooper bob") This will spawn a stormtrooper NPC named bob. After this, you will be able to control the NPC as long as it has a name, with the Control cheat code. This also works with droid NPCs. (Example: "control bob")
- The title screen of Star Wars: Jedi Knight: Jedi Academy shows Aurebesh characters in the background which transliterates to:
- In the mission to Tatooine, when you release the Raven's Claw and the Millennium Falcon from the beams, Chewbacca shows up from the exit to tell you to follow. The door reads SALIDA (Spanish for "exit") in reversed Aurebesh.
- Outside Lannik Racto's office, the inscription on the gate reads OFFICE. The small yellow brown pillar reads just Pillar.
- Numerous objects bear labels that translate to literal descriptions of the object. On Hoth, for example, large crates are labeled HOTH CRATE and chairs in the Echo Base command center are labeled REBEL CHAIR.
- During the Second Mission to Coruscant, a number of billboards flank the path taken by Jaden Korr. One of them reads, "Many ways exist to lose your money here...many..."
- The prisoners wear clothes with text saying "CREW."
- In the main menu, things such as Load or Options are also written in aurebesh if highlighted with mouse.
- The player's character, Jaden, is customizable, and players have the option of being male or female of different species including a Twi'lek female, Kel Dor male, Zabrak female or Rodian male (as well as Human of either gender). You can also choose from several lightsaber hilts and blade and clothes colors (Skin Color For the Twi'lek).
- Halfway through the game, players can choose to wield one lightsaber, two lightsabers, or a double-bladed lightsaber. The latter two can both be wielded as single blades; the player can select to ignite only one of the two blades interchanging between one and two whenever they wish.
- There is a mission selection screen with five missions on it. You can decide which one you want to do. After you have completed four it asks you if you want to complete the fifth or skip it. Then there is another story mission, and then five more missions.
- New moves including katas, wall gripping, and acrobatics, which add a new level to combat, instead of the standard slashing and cleaving. Depending on your type of lightsaber(s), you can have additional defensive and offensive moves.
- Two new weapons: DL-44 heavy blaster pistol and Stouker concussion rifle.
- New gametype: Powerduel—Players join as an individual or as a team of two. The individual has more health and Force power in exchange for being at a disadvantage in numbers.
- Siege Mode: Players work to complete goals and stop the other team from completing their goals.
- Enhanced rendering of the Quake 3 Engine.
- Force powers are now selectable, and you can't learn all of them. Instead, you gain your universal Force powers automatically, but with each mission you choose to add a point to either a light- or dark-side-themed Force Power. New powers include Force absorb and Force protection, Drain Life, Force rage, and Force sense. All of the classic powers (Force Push, Force Pull, Force Jump, Force speed, Mind trick, Force Choke, Force lightning), are still selectable.
- Force Sense can now be used in story mode, and is not just a multiplayer exclusive. It is even needed to solve puzzles.
Following The Walt Disney Company's decision to close LucasArts on April 3, 2013, the developers at Raven Software released the source code for the game on SourceForge under GNU GPLv2 licensing. However, the source code for both games disappeared from SourceForge without explanation. SourceForge later explained that Raven had requested the removal of the code, which may have been due to the presence of proprietary code that was not intended to be made public. Later, based on the source code released by Raven, a group of coders by the name of JACoders created OpenJK, an effort to improve the game engine, without any modification to gameplay, for both Star Wars: Jedi Knight II: Jedi Outcast (single player) and Star Wars: Jedi Knight: Jedi Academy (single and multiplayer), maintaining full backwards compatibility with the existing games.