MAIA encounters Knuckles and Amy while searching for Sonic at the Abandoned Research Facility. After Knuckles tells it where Sonic is, it finds Sonic and Tails while they were looking for one of the Chaos Crystals. MAIA then opens a portal for Sonic to enter the past. As Sonic and Tails are about to enter, they are distracted by Shadow who challenges them to a fight to prove he is stronger. Following a battle that took them through different time periods through MAIA's portals, Sonic kicked Shadow into a portal, which MAIA replied was leading to the near future separate than theirs. The two enter the portal once MAIA stabilizes it.
In one cutscene, Q-N-C's dialogue suggests that MAIA is mass-produced.
An unused character profile for MAIA in Sonic Boom: Rise of Lyric says that her name stands for "Manufacturing Artificial Intelligence Administrator" and that she is the boss program that runs Lyric's Weapon Facility.