The game is divided into three chapters. The first chapter deals with Zwei being turned into a killer and has two main "routes" to follow, the Ein route and the Claudia route. No matter which route is chosen, the chapter ends with Scythe escaping and Ein presumably dead, unless one opts to escape back to Japan. The second chapter starts off one year after the events in the first chapter, and deals with Claudia's plan to bring the Godoh group into the organization, Scythe's revenge, and the introduction of a new character, Cal Devens. It contains the Cal route and the final Claudia route.
In 2010, Nitroplus announced the game will be remade for the Xbox 360 featuring the same scenario but based on the designs created for the anime series from Bee Train. Character designs from artists Minkao Shiba, Yoko Kikuchi, Tomoaki Kado, Yoshimitsu Yamashita and Yoshiaki Tsubata were introduced into the 360 version. In addition to the design adaptations, the cast of the anime series also reprised their roles for the newer/updated version. It was originally planned for a Winter 2011 release, but was delayed due to unforeseen complications. The game has been released on October 25, 2012 and ported on PC on August 30, 2013.
Unlike standard visual novels where you usually focus on a single girl near the start and delve more into her story, the story is much more interleaved in Phantom of Inferno. The game is divided into 3 chapters, and each chapter has different routes which will affect the sequence of events, as well as vary the scenes and endings that you will get.
To get on Ein's route, simply think about her on the first night, and call to her on the night of the final test. After returning from the body guard assignment, save Ein, do not let her go, and console her in the motel room. At the final confrontation at the compound, Reiji will attempt to shoot Scythe, but Ein jumps into the way, taking the bullet for him. Scythe then escapes.
To get on Claudia's route, you must learn to drive the F40 and sleep with Claudia during the body guard assignment. You must also choose to save Ein, but instead, plan to return to Inferno. During the final confrontation at the compound, Reiji will be shot at by an unknown sniper and both will play a game of cat and mouse to try and discover each other's position. Seeing someone's shadow behind him, Reiji turns and fires, hitting Ein, who had not fired even though she had gotten the drop on Reiji. Scythe then shoots Reiji and is about to finish him off when Lizzie arrives and saves his life. Scythe still manages to escape however.
The events in chapter 2 will be decided by whose route you took in chapter 1, as well as whether you partially or completely finished them. Cal's path is necessary for several of the chapter 2 endings.
Cal's route is very strict because a single deviation will cause the game to treat it as if you had never met Cal in the first place. Generally speaking, all the options in Cal's route will be "Cal or something else", and you must pick the Cal-related option (such as going shopping with her). If you turn her down once, or simply choose to not trust her at the beginning, then the story immediately assumes that you never met her in the first place, which, depending on your decisions, may seem rather odd (Choosing not to go shopping with Cal for instance, completely removes her appearance from any further scenes, almost as if she went shopping but never came back).
The exception is if you chose not to accept Cal's confession, in which case she will still show up in the game afterwards. However you will not be able to get the Southbound ending and will be relegated to a dead end where Ein shoots you in the desert warehouse.
If you completed Claudia's path in chapter 1 and start on Cal's path in chapter 2, then you will have to pick which path you wish to complete. You will have the option to go to Claudia's house (which will put you on Claudia's route in chapter 2) or not (Cal's route).
Getting to chapter three may be tricky, since it requires a specific set of circumstances. You must have completed both Ein and Cal's paths, confirmed the sniper's identity, and discovered the identity of the attackers at the harbor. After the loft is bombed, you must "Hide". After this you will meet up with Ein at the warehouse and escape southwards. However, Cal is still alive and thinks that Reiji lied to her. She is then discovered by Scythe, who encourages this belief, and which will form one of the crucial plot points of chapter three.