Squaresoft (1986–1993)
In 1986, Gebelli became interested in developing games again and met with Doug Carlston, his friend and owner of video game developer Broderbund. Carlston told him about the rise of the Nintendo Entertainment System and how he should start creating games for the console. Gebelli was interested, and so Doug offered to fly to Japan with Nasir and introduce him to his contacts at Square. Nasir had the opportunity to meet with Masafumi Miyamoto, founder and president of Square, who decided to hire him. The programmers, especially Hironobu Sakaguchi (a long-time fan of Gebelli's work), were aware of Nasir's reputation and were excited to have him join.
Famicom 3D System
While at Square, Nasir programmed the game Tobidase Daisakusen for the Famicom Disk System, released in the United States in early 1987 as 3-D WorldRunner on the NES. 3-D WorldRunner was a pseudo-3D third-person platform game where players move in any forward-scrolling direction and leap over obstacles and chasms. It was also notable for being one of the first stereoscopic video games. His second Square project was Highway Star (Rad Racer in the U.S.), a stereoscopic 3-D racing game also designed for the Famicom 3D System in 1987. According to Sakaguchi, Square initially hired Gebelli for his 3D programming techniques, as seen in 3-D WorldRunner and Rad Racer. At the time, Gebelli did not know any Japanese and had no translator, so it was initially difficult to communicate with Sakaguchi. There were only three staff members working on both games, Gebelli, Sakaguchi, and graphic designer Kazuko Shibuya. Both games were commercially successful, selling about 500,000 copies each.
Final Fantasy
Gebelli then teamed up with Sakaguchi, Nobuo Uematsu and Yoshitaka Amano as part of Square's A-Team to produce Final Fantasy, the first entry in the popular Final Fantasy series. A role-playing video game released for the NES in 1987 in Japan, it featured several unique features, a character creation system, the concept of time travel, side-view battles and transportation by canoe, boat and airship. It also had the first RPG minigame, a sliding puzzle added by Gebelli into the game despite its not being part of Squaresoft's original game design.
He went on to program Final Fantasy II, released in 1988, introducing an "emotional storyline, morally ambiguous characters, tragic events". He also made the story "emotionally experienced rather than concluded from gameplay and conversations". The game replaced traditional levels and experience points with a new activity-based progression system that required "gradual development of individual statistics through continuous actions of the same kind". Final Fantasy II also featured open-ended exploration and an innovative dialogue system where players use keywords or phrases during conversations with non-player characters.
Gebelli went on to program Final Fantasy III in 1990, which introduced the job system, a character progression engine allowing the changing and combination of character classes. Midway through the development of both Final Fantasy II and III, Gebelli returned to Sacramento, California from Japan due to an expired work visa. The rest of the development staff followed him to Sacramento with materials and equipment needed to finish game production.
Secret of Mana
After completing Final Fantasy III, Gebelli took another long vacation and later returned to work on Seiken Densetsu II (released as Secret of Mana in the U.S.), the second entry in the Mana series, released in 1993. The game made advances to the action role-playing game genre, including its unique cooperative multiplayer gameplay. The team who created the game had worked on the first three Final Fantasy titles: Gebelli, Koichi Ishii, and Hiromichi Tanaka. The team developed Secret of Mana to be a launch title for Super NES's CD-ROM add-on. After Sony and Nintendo backed out of making the console, the game was changed to fit in a standard Super NES game pak.
The game received considerable acclaim for its innovative pausable real-time battle system, stamina bar, the "Ring Command" menu system, its innovative cooperative multiplayer gameplay, and the customizable AI settings for computer-controlled allies.