
Sonic and his friends return home as Sonic and Knuckles argue over whether their group is named "Team Sonic" or "Team Knuckles". As Sticks makes a long, disorganized speech about teamwork, Shadow goes his own separate way. Refusing to concede defeat, Lyric attempts to destroy them with an experimental weapon, but Shadow intervenes and sends Lyric falling to his death through a floor hatch that Sonic opens. Sonic and company eventually catch up with them and rescue Amy before confronting Lyric aboard his airship. Meanwhile, Lyric interrogates Amy to get the translation of the manuscripts she found. Along the way, they encounter Shadow, whom Sonic proceeds to defeat in a race, freeing him from Lyric's control Shadow then sets out to avenge his enslavement. Together with Tails, Knuckles, and Sticks, Sonic traces Amy's footsteps in hopes of saving her from Lyric's clutches. When Amy disengages to contact Sonic, Lyric, taking advantage of the distraction, incapacitates and captures her. She finds a secret ancient language and manuscript detailing the history and whereabouts of the crystal, but while trying to decipher it, she is ambushed by Lyric, leading to the game's opening scene. Meanwhile, after rescuing Sticks from a rockslide, Amy enters a set of ancient ruins to collect research. While working, Lyric is confronted by Shadow, whom he captures using a mind-controlling device. In the present day, Lyric escapes from his imprisonment and begins searching for the lost fragments of the crystal to obtain ultimate power. However, his fellow Ancients destroyed the crystal and detained him in stasis. The game's backstory is explained in a comic tie-in included in the game: millennia ago, the evil serpentine cyborg, Lyric the Last Ancient, attempted to conquer the world using a powerful crystal. Throughout each stage, players can locate crystal shards, required to progress through the game, as well as parts that can be used to buy upgrades. Sonic is able to perform a mid-air dash which can break blue barriers, Tails can fly up air currents and use various gadgets such as submarines, Knuckles can climb on walls and burrow underground, and Sticks can throw a boomerang that can be controlled mid-flight. Each character also has unique skills required to access certain parts of each stage. Each character is able to use a homing attack to home in on enemies and an Enerbeam which lets them swing across gaps and remove enemy shields.

Through the course of the game, players gain access to four playable characters- Sonic, Tails, Knuckles, and Sticks-and can instantly switch between them during gameplay. Shattered Crystal is largely a side-scrolling platform game, which features a stronger emphasis on exploration compared to previous Sonic titles. The two games together formed the third and final part in Sega's exclusivity agreement with Nintendo, following Sonic Lost World and Mario & Sonic at the Sochi 2014 Olympic Winter Games in 2013. Along with its Wii U sibling Sonic Boom: Rise of Lyric, Shattered Crystal is a spin-off of Sega's Sonic the Hedgehog franchise and is a part of the Sonic Boom sub-franchise, which consists also of an animated television series, whose games serve as its prequels. Sonic Boom: Shattered Crystal is a 2014 action-adventure game developed by Sanzaru Games and published by Sega for the Nintendo 3DS.
