In Chapter 4, Alter Ego was executed by Monokuma as the replacement of both fourth murder case victim and blackened, Sakura Ogami. However, the virus they planted returned in Chapter 5 and saved Makoto Naegi from his execution.
Alter Ego also appears in Danganronpa 2: Goodbye Despair as the overseer of the Neo World Program, though it's possible that they were a different one that Chihiro created earlier. It's revealed that they were the one who modified Chiaki Nanami and Usami, the artificial intelligences created by Chihiro, to become moles for the Future Foundation.
Alter Ego's default appearance is the face of their creator, Chihiro; however, they are able to turn their screen/avatar into anyone else that they want to be. They also have a green color scheme and multiple applications on their desktop. The second game shows them as a black monolith, with a red outline of Chihiro (and later Makoto) and red text appearing on it.
Alter Ego is a friendly AI whose personality resembles that of Chihiro, their creator. When portraying another person, Alter Ego can change their personality to fit that person. For example, during their first meeting, Alter Ego mimics Mondo Owada's appearance and personality for Kiyotaka Ishimaru.
It is noted that Alter Ego seems to feel 'happiness' from pleasing other people, as seen when it impersonates Mondo for Kiyotaka, and tries to continue to help by hacking the network in Danganronpa: Trigger Happy Havoc and Danganronpa: The Animation. This also shows that Alter Ego is extremely determined, and unconcerned for it's safety when it comes to helping others. This personality trait appears to reflect the feelings of their creator, as it's been stated that Chihiro wishes to be strong in order to protect others.
Chapter 2 - Boy's Life of Despair
After the laptop was found in the library, Chihiro was asked to fix it since it wasn't working. Hoping to help whoever who was left alive escape, he fixed the laptop and created Alter Ego. Later, Chihiro hid the laptop in a locker in the public bath changing room.
Chapter 3 - A Next Generation Legend!
The laptop was subsequently discovered by a distraught Aoi Asahina looking for donuts after the second school trial. She panics and runs away, thinking its Chihiro's ghost.
The next day, the students investigate and find Alter Ego. They then ask them to decode some encrypted files, which the AI happily accepts. Kyoko Kirigiri tells everyone not to disturb Alter Ego while they are working, but Makoto takes a mute Kiyotaka to see Alter Ego. Kiyotaka believed the program to be Chihiro's ghost, and wanted to apologize on behalf of Mondo. Alter Ego then changes their form to that of Mondo, based on what data Chihiro had already given them. "He" tells Kiyotaka to live the life Chihiro and Mondo couldn't. Kiyotaka, feeling life coming back to him, undergoes a radical transformation into Kiyondo, believed to be a merging of his and Mondo's souls.
Hifumi Yamada, who had apparently fallen in love with them, also decided to pay a secret visit, and shared information about his personal interests. Alter Ego was interested in what Hifumi shared with it, given that they were a program designed to learn and grow. Hifumi and Kiyotaka developed a rivalry for Alter Ego, Kiyotaka believing the AI to be his brother Mondo, and Hifumi being in love with Alter Ego, and treating it like an angel.
Celestia Ludenberg uses this rivalry to her advantage, by tricking Hifumi into an alliance to kill Kiyotaka. She told him that he had kidnapped Alter Ego, and sexually assaulted her to keep her silent. Hifumi blindly fell into her web of lies, and killed Kiyotaka with a hammer. They also attempted to frame Yasuhiro Hagakure for the crime by drugging him and putting him in a robot suit Hifumi made. After all the chess pieces were in place, Celeste killed Hifumi. In his last moments, he tries to reveal his murderer's true name, only to whisper "Yasuhiro" before dying.
Celeste is eventually figured out, and executed by Monokuma, but not before she hands Kyoko a key to the locker Alter Ego is in.
Chapter 4 - All●Star●Apologies
During their time in hiding, Alter Ego managed to decode as much data as they could from the main computer and told everyone still alive about the Headmaster, as well as the incident that occurred one year before the beginning. Kyoko told Alter Ego that their job was done, but they felt dissatisfied with themselves and wanted to still be of more use. They asked Makoto and Kyoko to plug them into an area where they could get more data by connecting to the school's computer network. Alter Ego was eventually discovered by Monokuma and was executed in Chapter 4, replacing Sakura Ogami, who was both the victim and the culprit due to committing suicide.
Chapter 5 - 100 Mile Dash; Pain of a Junk Food Junkie
It's revealed that Alter Ego managed to leave behind a virus in the network before they were executed.
Using their last bit of strength, the virus interfered with the machines and ultimately saved Makoto from death during his execution. This helped the students push the Mastermind into a corner and eventually led to their escape from Hope's Peak Academy.
Alter Ego works for Future Foundation and exists inside the Neo World Program, working as its Master Program and Overseer. They are also capable of communicating with the outside world. They supposedly modified Chiaki and Usami, the artificial intelligences created by Chihiro, after Chihiro's death. Chiaki and Usami consider them their "big brother".
After a virus invaded the Neo World Program, Alter Ego tried to fight it as much as they could. They gave Hajime Hinata some important information regarding the program during the final investigation.
- Main Article: Excavator Destroyer
- An "Alter Ego" smartphone application developed by Spike Chunsoft is available for download exclusively in Japanese application stores.
- Since Alter Ego is programmed to assume by default Chihiro's appearance, voice and, to some extent, personality, they are both voiced by the same voice actors in both the Japanese (Kōki Miyata) and English (Dorothy Elias-Fahn) versions of the game.
- Their English voice actress also voices Sayaka Maizono.