Chapter 2
The End of a Long Dream: To get this ending, the player must do Claudia's path in chapter 1 and 2, but not meet Cal, and then do not shoot Lizzie when she draws her gun. Reiji then goes to the warehouse in the desert and waits for Ein to find and kill him, which she does, lamenting his death and the scar in her heart.
Southbound: To get this ending, the player must complete Ein's path in chapter 1 but not fully complete Cal's path in chapter 2, and must also identify the sniper and attackers at the harbor. Reiji goes to the warehouse in the desert and waits for Ein to kill him, but Ein asks Reiji to kill her instead, as Scythe has no more use for her and she sees no other purpose in her life. Neither is able to kill the other, and finally they vow to head south this time to start a new life together (having headed north on their failed attempt to run away from Inferno in chapter 1). This can be considered Ein's happy ending, and is more or less the same as the path to chapter 3, but since Reiji has no complete relationship with Cal, the two of them simply head south to start a new life together.
Fugitives: This ending requires the player to follow the full Cal path in chapter 2 but NOT finish Ein's path in chapter 1 or Claudia's path in chapter 2. After the loft is bombed, the player must select to "Hide". After this Cal will arrive back from her shopping trip and Reiji vows to escape with her and start a new life together.
Vengeful Spirits: This ending requires the player to follow the full Cal path in Chapter 2. After the loft is bombed, the player should select the option to "Kill everyone". Reiji goes berserk and storms Inferno HQ, killing over 20 men and McGuire in the process before dying of multiple wounds, as he believes Inferno has taken Cal away from him. However, Cal was not in the apartment during the explosion. She waits faithfully for him to return as he promised to, finally accusing him of lying to her after the third morning.
At this point, the alternative option "Hide" simply causes Reiji to go hide at the warehouse in the desert and wait for Ein to kill him, which she does not do. Instead the two flee to Japan; progressing the game from Chapter 2 to Chapter 3. It is nearly identical to "The End of the Long Dream" ending.
From Atop the Hill: There are two variations of this ending. Both require the player to finish Claudia's route in chapter 1 and 2 completely and finish off by selecting "Shoot Claudia" at the hangar. One version requires the player not to have met Cal or broken off the relationship early on, and the other requires the player to have gone as far with the Cal route as possible in addition to Claudia's route. Reiji remembers that he vowed to survive at all costs, and shoots Claudia at the hangar, bringing her body and the disk back to Inferno.
Five years later, Inferno has united all the underworld kingpins in America and is poised to conquer the new century. Then all the kingpins are shot by Scythe's elite team, the Zahlen Schwestern, as part of Reiji's plan to take over Inferno and manipulate the criminal underground for himself. He was able to do this because the Zahlen Schwestern were created based on Ein's data, and as he once tried to communicate with Ein, he managed to communicate with the Zahlen Schwestern and get them to trust in him. Reiji then shoots Scythe. If you also did the Cal route, then Lizzie reports that Cal managed to assassinate McGuire in Colombia. Reiji gives her the title of Phantom, as she became his best assassin in the 5 years since the hangar incident. If the player did not meet Cal, then she is simply not mentioned. In both variations, Lizzie is disgusted with what Reiji has become, leaving the organization for the country to start a bar. Reiji finally visits Claudia's grave at a small cemetery on top of a lonely hill, looking down at the city below.
If the player is playing the DVD version, the player will get the first part of the ending password here. The ending password unlocks several extras such as the various production trailers, TV commercials, nearly all of the FMV sequences, and the sound track. However, the English translated DVD version has the "Gun Gallery" locked out for unknown reasons. The gun gallery is used to showcase all the guns that are in the game.
The Woman in the High Castle: Unlike "From Atop the Hill", this ending has only one version regardless of whether the player met Cal or not. Reiji chooses to accept fate and allow Claudia to shoot him, and helps her by pretending to try and shoot her. Reiji ends up dying in Claudia's arms, telling her that she needs to live and get back all the things stolen from her, and to take revenge on Inferno.
One year later, Claudia has hooked up with the new No.2 man of the Gambino family, and is slowly manipulating both him and the family for her own purposes. However, she still keeps the .38 special cartridge from the bullet that she shot Reiji with, and can't seem to get rid of it or forget what she did that morning in the Hangar. As she stands at a window looking down at the city below her, she vows to become stronger or she will lose to someone like her previous, merciless self.
This ending will give the player the first part of the ending password as well.
Chapter 3
Road of the Cerulean Sky: This can be considered Ein's "True Ending". To obtain this ending, do not fully complete Mio's path in chapter 3, and at the final choice, choose to go after Elen. Reiji will find her in the church, and after a tearful reunion they get married right there and then. Reiji insists on fighting Cal, and manages to get Elen to promise him to leave and wait for him, and that he would definitely return to her. Cal arrives at the appointed time, and takes out the pocket watch that Reiji bought for her 2 years ago from a street vendor while the two of them were preparing for the counter snipe operation. Setting it on the altar, she opens it, starting the music, and sets the stage for the duel. When the music stops, both go for their guns, but Reiji is faster and Cal suffers a fatal wound. In the end, as she lies dying in Reiji's arms, Cal forgives Reiji for everything. Shortly after, the Godoh group sends 19 men to assault the church. Reiji nearly runs out of ammo, but is saved by the sudden appearance of Elen, and they manage to escape.
Scythe arrives after the sun has set with the Zahlen Schwestern and manages to get Shiga to back off and let him handle the situation. In the ensuing battle, Elen shoots Scythe, and all the members of the Zahlen Schwestern are killed. When the semester starts, Mio, who was rescued from the ruins by Shiga (who of course insisted it was a kidnapping motivated by money), can't help but feel it was a dream. Regardless, she resolves to live her life and meet the challenges of tomorrow.
Meanwhile, Elen and Reiji start a long and arduous investigation into Scythe and Elen's past, trying to discover her identity. While doing so, in the 2012 remastered edition, it is revealed that Lizzie, who was shot by Cal in the duel for Mio, has survived and killed McGuire, effectively putting an end to Inferno, once she heard about McGuire's intentions to send men after Elen and Reiji. They eventually trace her back to a Hong Kong brothel that handled young girls, and then to Ulan Bator, Mongolia, where the trail runs cold. Eventually a young translator gives them the advice to go to the grasslands and look at the sky to find Ein's homeland. With no other options, they do that, and Elen discovers that this place really is her homeland, and she ends the investigation, stating that she is satisfied just to be here with Reiji.