Star Wars: Knights of the Old Republic II: The Sith Lords is the sequel to Star Wars: Knights of the Old Republic, which was widely regarded as a major commercial and critical success, though there has been some controversy regarding the cut content. LucasArts pressured developer Obsidian Entertainment to finish the game for a holiday 2004 release, leading many to speculate that the development had been rushed. Due to this, the actual game contains a sizable number of bugs, which occasionally cripple game play. Also, some of the content from the game proper appears to be missing; however, much of it can be found inside the game files.
The originally planned ending would have provided in-game fates - and in many cases, deaths - for all of the characters who travel with the main player character. In-game, the game ends with Darth Traya revealing the party member's futures. By explaining their futures, instead of showing the events leading up to the finale, it leaves just what happened to the designers of KOTOR III.
In a gesture to the fans, Obsidian provided the PC version of the game with many resources meant to be used for the original ending, such as screen plays, voice-acting, etc. The aforementioned pressure forced Obsidian to abbreviate the ending, also forcing them to petition LucasArts themselves for a content patch which would restore the unused content, though LucasArts denied the request.
They were extracted and arranged by two users of the Obsidian Forum Community known as "HighPriest" and "Aurora" to produce The Sith Lords Restoration Project. While the files do not resolve everything, they do clarify what would have happened to many of the members of your party, and elucidate many in-game events.
- Repairing the Hawk - While still trying to find a way to Onderon, the player can ask Atton how the repairs are going.
- Atton Bath Jokes - When Atton describes Nal Hutta, Handmaiden/Disciple chips in about Atton not bathing.
◾The Red Eclipse Boarding - The Red Eclipse boards the Ebon Hawk. Handmaiden/Disciple/Bao-Dur was supposed to take note while in the cockpit. However, they are stopped by Kreia who incapacitates them and then throws a poison grenade down. Cahhmakt orders his men to throw the party into the cargo hold when stumbling upon the two incapacitated members.
◾Mandalore and the Ebon Hawk - After returning from Onderon for the first time, Mandalore was supposed to comment to the PC about the Ebon Hawk and ask where the PC got it from.
◾Bao-Dur's anger with Mandalore - After returning from Onderon for the first time, Bao-Dur asks the PC why he trusts Mandalore to be among them.
◾Mandalore reinforces his reasons - Mandalore will tell the Exile that the only reason he is with the PC is to gather the clans.
◾The PC dies again - the Party is upset because of what happened in the Jedi Enclave.
◾It is time - Kreia was supposed to come on board the Ebon Hawk and tell Atton that it is time for them to leave for Malachor (or Telos since she stops there first after Dantooine). Kreia takes the Ebon Hawk from Dantooine to Telos. Player is forced to find an alternate means of transportation to get there.
◾Reaching Out - the PC lies in the medical room unconscious. The player would reach out to the party members as they are a bit panicked and worried about losing the Exile and stopping Kreia.
◾HK-50s attack - Randomly, the HK-50s were to attack the PC. If HK-47 was in the party then he was to capture one and torture it to reveal the location of the factory on Telos.
◾Kreia isn't fond of droids either - After the player has witnessed the message from Bastila/Carth, Kreia will blast T3 with some force lightning in anger since the PC seemed to have a fondness for the droids.
◾Spar Practice - After Visas joins the party (and has a lightsaber) the player would be able to spar with her under Kreia's supervision.
◾Bao-Dur upgrades HK - Like G0-T0, the Remote and T3, Bao upgrades HK though at first he refuses.
◾Goto threatens Bao-Dur - If the PC knows that G0-T0 is actually Goto, then Goto will threaten Bao-Dur that he better take care of the remote before he finds a permanent solution. Presumably comes before Goto "repairs" the remote himself. Probably removed since the Goto/Remote destruction scene must be triggered and the player may not find out about Goto being a droid.
◾Meditation Envy Alternate Lines - When Atton watches the Disciple and PC meditate, Mira and Atton say some alternate lines including about Atton's mentality and behavior ("scratching his equipment" when nobody is looking)
◾Disciple's Choice - After Kreia reveals the truth about herself to him, she goads him into telling the Republic what's happening but in doing so, he'd endanger the Exile.
◾Bao-Dur and Mandalore's second discussion - Sometime after their first argument, Mandalore goes to Bao-Dur about how he destroyed the Mandalorians and activated the MSG.
◾The story of Canderous Ordo - After discovering that Mandalore traveled with Revan and the story of the helmet, the PC can ask T3 if he knew Mandalore. T3 displays a hologram and shows when Revan left (this isn't actually shown.)
◾Ratrin Vhek on the Ebon Hawk - During the Red Eclipse invasion, the PC can sell Ratrin Vhek into slavery.
◾Disciple's Distress Call - Before traveling to Telos, Disciple calls Admiral Onasi/Cede about the impending attack on Telos. Content suggests that he was originally supposed to be a pawn of Atris, referring to the contact as "mistress".
◾The Handmaiden's Choice - Currently, Handmaiden does not say if she has joined the party on her own free will or of Atris's. When Brianna joins the party, she claims that she believes the Exile was right about going to war. Kreia believes her and tells the player that they cannot take her back.
◾The Holocrons - Throughout the game, if the player is female, she'd find Holocrons in various places. She and the Disciple would examine them and would learn new abilities.
◾Atton lies to the player - When the PC asks about Atton's past, depending on the influence probably, Atton lies to the player and then tells Kreia about it.
◾Atton and T3 play Pazaak - Atton and T3 play pazaak. T3 apparently wins all games.
◾Atton and Kreia's Plot - After Atton confronts Disciple on the message he sent to the Republic concerning his whereabouts, Atton goes to Kreia and asks her why they allowed the Republic Spy on board. Kreia tells Atton to wait and the time will come when she'll call upon him.
◾Teaching Forms - After training the party members as Jedi and learning the forms for himself/herself, the player would be able to teach Saber Forms and Force Forms to the party members.
◾The Astrogation System Locked - After the player has viewed the message from Bastila or Carth and T3 has stopped HK-47 from viewing the navicomputer, the PC can ask T3 about the navicomputer and why it's locked.
◾The Council's Alternate Lines - During the Jedi Council hologram, there are three lines of alternate dialog from the masters concerning the awaiting echo from Malachor V and Revan's influence.
◾Handmaiden's Own Volition - Handmaiden claims she is joining you against the wishes of Atris and her sisters in her first appearance on the Hawk.
◾Kreia and the Ebon Hawk - After first meeting Kreia in the morgue, an alternate line has her refer to the docked ship as "The Ebon Hawk" rather than simply not naming it.
◾Peragus Equipment - There are unused items in the game files which are assumed to be mining utilities for Peragus: The Vibrocutter (similar to a Vibroblade though less powerful), a Guidon Beacon (a beacon used to stake claims on asteroids that can be used as a quarterstaff), and a Heavy Mining Laser (a Mining Laser similar to the Heavy Weapons from the original Knights Of The Old Republic).
◾Kreia Knows - When Sion arrives to Peragus II, Kreia was supposed to take note of his presence, saying "He has come".
◾Darth Sion knows Kreia - When Sion encountered the Exile's party aboard the Harbinger, he would say, "I came to warn you, Jedi. You know not what path you walk." An alternative line was "I have come for the Jedi."
◾Lt. Yima's Mission - Yima, the one Grenn always talks about, was supposed to give the PC a mission to expose a corrupt TSF officer in the Czerka docking bays. Probably connected to the alternate docking bays that can be seen.
◾Duros Thug - A random Duros thug simply attacks the PC for asking questions. This is probably due to the player asking around about the blaster. He just spawns in.
◾Batu Rem of the Genoharadan - the false Batu Rem is actually a Genoharadan disciple and makes it perfectly clear when he attempts to kill the PC.
◾Bounty Hunters of the Genoharadan - Luxa's Bounty Hunter contacts are actually Genoharadan agents hunting the PC.
◾Bao-Dur's return to Citadel Station - Bao-Dur was supposed to take the PC back to Citadel Station and then it'd be there that he'd track the Ebon Hawk to the polar ice cap instead of going through the Czerka base.
◾Czerka takes control - Czerka was to completely take over the modules, threatening the Ithorian herd. The PC is supposed to get to the communications station and call for help since the TSF can't do anything else. Probably connected to Jana Lorso's lines about taking over Citadel Station due to Onderon's secession from the Republic and because of that, Lorso lies to Citadel Station that the Telosian Council has entered an anti-Republic treaty with Onderon.
◾An option to see Carth - PC had the option of denying Carth an audience after saving Telos.
◾Corrun Falt's Plan - Infiltrating the main frame was not always an Ithorian quest. But the PC was supposed to learn from Corrun Falt that he had planned on exposing Lorso's dirty dealings himself, if PC had sided with Czerka. PC can help or expose Falt to Lorso. Exposing Falt to Lorso will result in Falt attacking the PC but then the Czerka guards kill him anyway.
◾Missing HK-47 and Bao-Dur - When arriving on Citadel Station due to the Sith Attack, Grenn notes that he thought he saw Bao-Dur disembark with the player, but he is missing. Atton also notices HK is missing if the HK Factory was triggered properly.
◾Atton and Bao-Dur take note of surrounding obstacles - Minefields, sentry droids, and mercenaries, Bao-Dur and Atton take note that all are present and that the PC needs to get around them.
◾The Crash - Atton is supposed to say a few lines as the shuttle from Citadel Station plummets into the ground. When the shuttle crashes again at the Ice Plateau, Atton makes it known that it wasn't his fault.
◾HK-50s congratulate the shooter - After the shuttle is shot down, the HK-50s tell the shooter of his excellent shot.
◾HK-50s Concern - When awakening on the Ice Cap, instead of the HK saying "There you are!" he was to say that he is glad that the PC is still intact.
◾I've come for my lightsaber - Atris wields the player's lightsaber in the final battle when she is torturing the Handmaiden.
◾Helping or not helping Atris was supposed to have an effect on cutscenes when leaving the polar academy.
◾The Handmaidens Mission - Before leaving, Atris summons the Last of the Handmaidens. She gives her the mission to accompany the Exile and she is not to tell her sisters. Alternate dialogue between Sisters and Atris (Last is not among us) reveals that Atris did tell the sisters herself that she sent the Handmaiden with the Exile.
◾Come, Last of the Handmaidens - The player was supposed to be the one to kill the Handmaidens and as a result, the Last attacks after killing Atris. Dark side option.
◾Kreia and Atris's alternate lines - Kreia's alternate lines when talking to Atris suggest that she asked for the Exile's exile, and they discuss the Sith Holocrons that Atris had gathered.
◾Handmaiden leaves with Kreia - After Kreia's discussion with Atris (or Handmaiden's fight) Kreia takes the Handmaiden to Malachor to prepare for Visas's arrival.
◾Handmaidens Fight - Instead of the Handmaidens just dropping dead when the Handmaiden walks in, they were to fight each other. The Handmaiden can either kill them or incapacitate them.
◾Atris' Promise to her servants - Provided the player follow a certain path of dialog after the Handmaiden is beaten by Atris, Atris informs the Exile that she promised that the Sisters may kill him for harming Brianna. The Handmaiden sisters attack the Exile.
◾Attack! - Player had the option of killing all the Handmaidens during the first visit to the Academy.
◾White/Black Corruption - Originally, Atris was supposed to be clad in black robes during the final sequences, as well as the corrupted Handmaidens. This was cut because it would be odd for Atris to conveniently have Sith/Dark Jedi Robes lying around.
◾The HK Factory - HK-47 discovers the location of the factory and goes there during the attack on Telos. He is forced to find a way into the actual factory and before that, deactivate his self-preservation program. He can activate the HK-51s and destroy them, have them turn to his side, turn the HK-50s to his side and destroy the 51s, or just blow them all up. His actions determine the final fate of Malachor.
◾Atris exposition - According to writer Chris Avellone, Atris was supposed to have two other cut-scenes in between planets.
◾Azkul Spies on the Militia - Right before the Battle of Khoonda (if player sides with Khoonda), Azkul will tell a trooper to tell him what he sees. They see the militia mobilizing. Azkul orders the captains to prepare their men.
◾The Attack on Khoonda - Battle of Khoonda was supposed to be larger then what is in the game currently. Including mines disabling/planting. Player would actually get to fight outside Khoonda, defending one of the entrances or simply attack Khoonda with Azkul (where you'd kill Zherron). Then it would move into Khoonda. Also, the player would deploy squadrons of troops to defend the administrator's door, the back door and the front door, based on their skills.
◾Kreia talks of the Enclave - When approaching the Enclave, Kreia is supposed to chime in about how you are to gather the Jedi here. Then again when the PC sees the rebuilt Enclave.
◾A Bounty for Vrook - Originally, the player could capture Master Vrook and Azkul would send him to Nar Shaddaa.
◾Suulru's Thief Problem - Instead of Jorran giving Suulru a bad deal with a vaporator, Suulru would have a problem with a thief stealing his farming equipment, thinking it's the salvagers. When completing the quest, the player can convince Suulru to change his ideas about the Jedi and how they messed up Dantooine.
◾Gerevick's Plans - Gerevick is supposed to contact someone inside Khoonda as the Exile eavesdrops. Presumably about how the Exile showed up and the threat to his claim on the dead salvagers in the Enclave.
◾A Lost Padawan - Kaevee, the thief from Suulru quest, is here, master of the laigreks. The player meets up with her and can either turn her to the dark side, kill her, or tell her to seek out real Jedi; not the mysterious holocron that she threw into the ruins before.
◾Disciple's Hidden Holocron - Disciple takes the Exile into a hidden, locked room in the Enclave and displays a holocron as well as recording of when the Exile left for the Mandalorian Wars, leaving a padawan without a master behind.
◾Kreia taunts each master - During the Masters infamous speech about how they must cut the Exile off from the Force, Kreia comes in as usual and throws them back. However, after she drains them, it's not over. Kreia was to ask each master how they could not have felt the echo and how close they were to giving up the Force but they failed. Kreia puts each of them in a crush, thus killing them.
◾Atris' absence- Brianna is supposed to arrive somewhat earlier, during the meeting and ask Kreia what was going on. She looks into the chamber and notices that Atris is not present and wonders why. She realizes Kreia is evil.
◾The Exile reads party members minds - When asked if he could not sense his party member’s thoughts, the party member with the Exile were supposed to have their mind read.
◾Visas's involvement - Visas notices Kreia is evil. After Kreia goes attacks player or masters, Kreia asks her to take her to Nihilus.
◾Disciple's proper greeting - When the PC enters the library in the Enclave and meets Mical, Mical will joke about becoming laigrek meat and how he is a self-styled disciple of knowledge. He would also explain exactly why he was in the library - due to laigreks coming at him in a full group.
◾Mandalore fights Esok - Originally, before fighting Esok, Mandalore was to insist to the exile that this was his fight alone. Only Mandalore would be player controlled during the fight, other characters would merely stand idle.
◾Bao-Dur's old friend - Tien Tubb and Bao-Dur were once friends and worked together in the Mandalorian Wars in a Republic ship's hangar bay. Bao-Dur recommends that Tien changes the Ebon Hawk's transponder codes.
◾Atton Doesn't Wait - When the Exile has gone off to meet Visquis in the Jekk'Jekk Tarr, if the player has low influence with him, he will not rush off to meet with her to tell her to be careful but instead just stay by the Ebon Hawk and leave the other party members there while he goes to the cantina.
◾Fighting to the Docks - After Atton has been attacked by the Twin Suns, he and two other party members attempt to rescue the Exile. The three would fight bounty hunters to the docks where they would meet up with Mira.
◾Vossk and the Genoharadan - Vossk makes references to the Genoharadan being on the Smugglers Moon.
◾A Dead Exile - Dessicus (Genoharadan) blows up the Jekk'Jekk Tarr and the party thinks the player is dead. Visas or Kreia will say that the betrayals will start to mount between the Sith.
◾Zez-Kai Ell's Rescue - Since Dessicus was originally supposed to be in the Jekk'Jekk Tarr (instead of Visquis) and he was supposed to set off an explosion. Zez-Kai Ell rescues the Exile from an explosive death, though the party still thinks the Exile is dead.
◾The Zhug brothers' Plan - The Zhug Brothers discuss the Exiles meeting with Visquis and plan an attack on the party members. When the player goes to rescue the Exile from Goto, the leader tells the others to follow the Ebon Hawk.
◾Adana - Adana thanks the Exile in the main refugee quad when she is returned to safety instead of not appearing at all.
◾Goto and Vogga - When entering Vogga's chambers, Goto comments that he should stay outside. ◾More than one Jedi on the moon - If Disciple or Kreia was in the party when Mira spied on the Exile, she'd make note of them.
◾Return of B-4D4 and T-1N1 - The pair from Telos Czerka Corp now guard the entrance to the room with the transponder codes. T3 attacks T1 and B-4D4 is grateful for letting him leave.
◾Opo Chano's Debt - When arriving in the slop house, Chano is supposed to be challenged by thugs for not paying his debts on Citadel Station. This happens when the Exile helps Chano get off Citadel station in the Czerka plot.
◾Fassa is a Toydarian - Fassa was probably originally supposed to be Quello, the Toydarian who greeted the Exile at the landing pad. And then at the docks, be the overseer instead of the Twi'lek.
◾Hanharr Broken - If Hanharr was the party member instead of Mira, then Hanharr would be found in the apartment in an incapacitated animation with Kreia looking down at him.
◾Sold or left? - If T3 was not sold to Kodin, then Atton would have said "What kept you?" when T3 returned from Vogga's warehouse.
◾Mira and the Exile plan things out - Mira, instead of knocking the player out, will explain Zez-Kai Ell early and have the Exile go in first instead of her stealing the environmental suit.
◾Fighting back to the landing pad - When the party members meet with Mira after the Exile has been captured, the Gand will attack them as they try to get to the landing pad to change the ID signatures.
◾Atton's Lap Dance - Atton was supposed to receive the Star Wars equivalent of a lap dance - a neck massage. Also, Atton is supposed to do sort of a confession of his "confused, stupid" love for the female Exile. During this scene, under the right circumstances, Atton instantly knows they are assassins from the clothes and concealed weapons.
◾Hussef's True Form - Hussef was supposed to have the appearance of a much elderly man with white hair instead of a generic male with red hair. ◾A rude little man - An NPC is supposed to try and score with a Twi'lek who attempts to shove off his efforts. Exile steps in to stop the man.
◾Find the Gand Quest - A Sullustan in the Gand section of the Jekk'Jekk Tarr: find the name of a great Gand warrior. Options were to lie to the Sullustan, find the Gand (with a high awareness) and then refuse to tell the Sullustan due to the Gand's request or tell the Sullustan anyway.
◾Spa Treatment at the Jekk'Jekk Tarr - The Twi'leks were supposed to be like the Twi'lek slaves at Davik's estate and offer steam baths and massages.
◾Environment suit stays on - The player would have the option to leave the environment suit on when speaking with Visquis. This exchange was moved to the arena to replace the Genoharadan. Visquis later would be able to capture the Exile and order the Ubese to take him to Goto.
◾Magic Eight Ball - In the Jekk'Jekk Tarr, there was to be a Weequay who had an orb where you can ask questions.
◾Mira's escape from the Jekk'Jekk Tarr - Instead of the Exile killing Visquis, it would be a party member and then Mira would lead them out of the Jekk'Jekk Tarr into her safe house. Also, Mira was to be held in some cell in which she says that Visquis will execute her, and where the party member would rescue her.
◾Dessicus of the Genoharadan - Obviously, the Genoharadan would be the organization beneath the Jekk'Jekk Tarr. Dessicus will challenge the Exile. After they fight, Dessicus blows the Jekk'Jekk Tarr up.
◾Kreia (speaking to Hanharr about another life debt) - Additional line from Kreia "The screams of your tribe of primitives, the scene of lying blinded with the huntresses' blaster at your skull, I shall make it so that is all you hear and see for the rest of your days." ◾Threatening Goto - When stumbling upon the control center, the player threatens to use a certain skill to dismantle his vessel, however, Goto says that his droids will just turn off the oxygen.
◾Goto's Orders - Goto will command his droids not only to activate the mines but raise the force shield, poison them and deploy guard droids. And finally, Goto notices the bounty hunters on his ship and gives the self-destruct order. ◾Time to abandon ship! - When the Bounty Hunters appear on Goto's vessel, Goto makes note of them and says it's time for him to take his leave. Also, HK-50s were supposed to be among the bounty hunters there. As well as more Zhug brothers (where the PC can gloat about killing them on Dxun)
◾Genoharadan are none of the bounty hunters' concern - One of the Zhug brothers will mention that the Genoharadan are also after the Exile during their meeting with Goto, and so Goto commands them to ignore them and says that they aren't of any concern.
◾A entire cantina was cut out from the planet. It was located near Vossk in the landing pad area. It is now just a door, but if you have or use Visas' force sight you can see the cantina for yourself.
◾Kreia's Premonition - On the first entrance to Nar Shaddaa if Kreia is in party she will stop and look around as though anticipating the troubles to come on the planet.
◾An Option to see Mandalore - Instead of player just killing the Mandalorians if he doesn't want to meet Mandalore, the PC has an option of leaving them alone.
◾Controlling the beast - somewhere within the tomb of Freedon Nadd, a scene where the Sith is controlling a beast and onlookers wonder how it's possible.
◾Kreia goes to the tomb - Kreia was originally supposed to be allowed to join the party that goes to the tomb. Cut so that it'd make sense with the Tobin scene in the Onderon Royal Palace where Kreia reveals the hiding place of the Jedi.
◾Vaklu's Entrance - If the player sides with Vaklu, then he should not have been waiting in the throne room but after the beast is dead, he arrives and runs to defeat Talia. Kavar rushes in to stop him. PC stops him. The options here are much more lenient to the light side in which the PC has the option of saying "Onderon would be better off".
◾Kadron's Fall - If the player sides with Vaklu, then when the PC arrives in the room where Kadron is then he will defend the terminal with his life.
◾The Sith Revelation - If the PC sides with Vaklu, the Sith will notice that the beasts no longer obey them. The Sith order Vaklu's death for the betrayal.
◾Party cannot enter - Before entering the tomb of Ludo Kressh, a party member chips in about not being able to move.
◾Apathy is death! - Currently, only Atton, T3, Bao-Dur and Disciple/Handmaiden/Visas appear in the tomb. Originally, all the party members were to be there to either defeat Kreia, or attack you.
◾Dustil Onasi - The dead Jedi in the tomb was supposed to be none other than Dustil Onasi. He was to be insane and then attack the PC.
◾Attacking yourself - At the end of the tomb after, before or during, the PC faces Revan, the PCs doppelgänger is also supposed to attack you. The doppelgänger has no Force powers but a considerable amount of strength. Currently, the copy merely stands there, then fades away after you enter the room.
◾Dvakvar Grahrk - There was originally going to be a Devaronian Jedi named Dvakvar Grahrk slowly turning to the dark side that was to join your party, but was later replaced by Disciple.
◾Fragile Alliance Falls apart - After Sion discovers the Exile is 'dead', he confronts Darth Nihilus on the Ravager. Sion claims that he is more powerful and never needed Nihilus's help. Nihilus, in anger, shows Sion that he is the more powerful one.
◾Tobin's message - Tobin arrives on the Ravager after Onderon and informs Nihilus about the Jedi at Telos to feed on.
◾Nihilus Fight expanded - Nihilus raises Visas and the PC up. PC then has the option of becoming his apprentice (lie or not). If lie then the PC and Visas attack Nihilus. If truth, PC turns on Visas and kills her. Either way, PC fights Nihilus. When Visas does die, Mandalore chips in with some dialogue and the PC can just leave her to die alone or mercy-kill her.
◾Mandalore and Visas - Mandalore and Visas tell each other not to betray each other. Later, Mandalore is hurt and Visas heals him and Mandalore tells all about what Revan did to him.
◾Originally the player was allowed to leave the Ravager without replacing the broken proton core. This results in the Ravager crashing into Telos IV and exploding.
◾Surik would have meditated in order to findout where Nihilus and Sion came from. She would have had a vision that featured her companions talking to her, their voices blending together, and it would have lead her to Malachor V.
◾Sion travels to the Smugglers Moon - Sion announces that he will travel to the Smugglers Moon (while observing a hologram of the Exile) himself to see if the Exile is truly dead.
◾Mandalore walks the taboo world - Visas and Mandalore were supposed to walk Malachor V together based on the loading screen to module 901MAL.
◾What Mandalore knows of Malachor - The player was once supposed to be able to take party member(s) with her to Malachor. The player could ask Mandalore what he knows of the planet. If player should "warp" to 902MAL with Mandalore in the party in a different location in the game, then it is still possible to hear his response.
◾Spare me? - Kreia puts Sion into a force choke and shows him that his strength is as meaningless as the strength of her cut-off hand.
◾Sion reports the Exile's arrival - After crash landing on Malachor V, Sion goes to Kreia and tells her that the Exile has arrived. Kreia tells Sion to bring her/him before her.
◾Hanharr and Mira - Hanharr was to slam Mira into the rock wall before their fight. If Mira was a Jedi, then Hanharr makes note of it and how the gray female told him that she claimed the title Jeedai. After the fight, Mira can ask Hanharr to lead her to Kreia. Hanharr says he will do so though he believes that Kreia will kill Mira and thus end both of his debts.
◾HK-47's interference - Depending on the choices in the HK factory, HK-47 shows up during the Remote/Goto confrontation. Either the HK50/51s come in and then HK blasts Goto or Goto would have taken control of HK and then HK would have blasted the Remote.
◾Atton's Grudge - Atton tells the Disciple how he lost what mattered to him. Disciple and Atton fight. Triggered by Atton's alignment.
◾A powerful crystal - When entering one of the cells, the player can find a crystal of a dead Jedi.
◾Handmaiden's Grudge - Handmaiden tells Visas how she seduced the Exile. Handmaiden/Visas fight. Triggered by whatever happened on the Ebon Hawk (if Handmaiden became angry at PC)
◾Two Paths - When the PC enters the academy, Kreia tells Sion of the PCs choices to save the party or just slaughter the way to Kreia.
◾Atton and Darth Sion - Atton and Darth Sion fight (player controlled). If wins, Atton lives. If lost, Atton was to have his arm chopped off and then Sion would torture him. Triggered if Atton is LS.
◾Atton's Death - Should Atton have lost to Sion, Atton dies in the players arms. Both male and female though the female version, he confesses his love.
◾Atton lives - Atton can live if he won the fight with Sion. He and the PC simply leave the Trayus Core together.
◾Handmaiden/Visas want to go - Handmaiden or Visas ask if she can go with the Exile wherever he is going. However, the PC tells them that they cannot.
◾Leaving the Republic to die - Another choice for the PC was to leave Malachor V and then leave the Republic to die.
◾The Party Attacks - The party plan an attack on Kreia. They attack Kreia who disposes of them easily after taunting them a bit.
◾Darth Traya is Atris - Instead of Kreia being at the core, it'd be Atris in her dark robes.
◾In the Trayus academy - On the map under the start menu, the doors leading to the "Trayus Crescent" are labeled as "Trayus Prison Cells".
◾Hanharr's Sacrifice - Presumably, if the player has Hanharr in the party and Malachor V is being destroyed, Hanharr would throw the player onto the Ebon Hawk. Hanharr would then die with Malachor V (which players and fans may remember as Chewbacca dying a similar death to save Anakin Solo).
◾Bao-Dur's sacrifice - In the game files, one of Bao-Dur's lines is "Make my sacrifice matter". According to Chris Avellone, Bao-Dur dies during "the attack on Telos to help HK-47 get to the HK-50 factory and shut it down to save the planet".
◾Several items were cut from the game. These include the Peragus items mentioned above, and the Prima Guide mentioned at least three items to be cut from the game: Malak's Ligthsaber (a standard, non-upgradable lightsaber with a violet crystal), Visas Marr's Lightsaber (Visas was to keep her lightsaber after her initial duel with the lightsaber and would use it uniquely to herself) and Bastila's lightsaber (note: Malak's Lightsaber and Bastila's lightsaber were seemingly only found in the guidebook and not in the game, and Bastila's saber was not mentioned in the equipment guide (while Malak's saber was). Therefore, it is unknown whether or not they were ever in the game).
A team of modders from the KOTOR and KOTOR II modding community using tools from Holowan Laboratories  have started a project to restore the appropriate missing content and release it as a mod.
The main restoration mod was called "The Sith Lords Restoration Project" and was in development by Team Gizka. It would have restored almost all of the cut content (apart from M4-78). However, in early 2010 Team Gizka dissolved. No one knows what happened but all work has stopped and all contact has been lost with the team. As of today there is only a half completed beta floating around torrent sites.
Another team of modders (Team Exile) encouraged by the efforts of Team Gizka plotted out and considered restoring the majority of content TG is not touching. Their project was called "The Sith Lords Restoration Project II: The Un-Restored Content." However, after problems concerning the team's leader Darth Balor - including accusations of plagiarism, the team disbanded.
Several months after the trouble with Darth Balor, the project was picked up by a user called Pikmin and the name was changed to The Sith Lords Content Restoration. On February 28th 2009, Pikmin was exposed as being Darth Balor.
The cut planet M4-78 has been restored by a modder called Darth Stoney, and has been made public on The Knights of the Old Republic FileFront website, and can be downloaded here. A new, heavily expanded version of Darth Stoney's mod called M4-78 Enhancement Project has been developed.
Stoney also teamed up with Zbyl to create their own mod called "The Sith Lords Restored Content Mod", which reintegrated all the cut content back into the game. It was completed as of March 14, 2010 and can be downloaded at Filefront. Version 1.7 was released 19th October 2010. So far it is the only large scale restoration mod to have been fully completed with regular updates being added. The final 1.8 patch, which restores all the content planed TSLRCM was released on the 25th of July, 2012. A version of the M4-78 mod called M4-78EP was released on December 28th and is compatible with TSLRCM 1.8.2.