This Game is based on the menu, gameplay and misc. of Shadow: The Hedgehog.
You will have two Mission Characters follow you around and give you clues to complete the stage, in Shadow, you had mostly Sonic and Rouge as your hero Mission Character and Dooms Eye and Dr. Eggman as your Dark Mission Character But it all Changes here, in Knuckles your main hero Mission character is Tikal the Echidna and Sonic, your main dark mission character is Chaos Zero and Dr. Eggman.
Instead of guns and alien weapons you will find upgrades for Knuckles' fists, at the end of every stage there is a goal ring, either empty or containing a shard of the Master Emerald, in Shadow you collected the Chaos Emeralds but in Knuckles you collect shards of the Master Emerald because Eggman destroyed it at the beginningso Chaos could be released along with Tikal
In Shadow the bosses were either Eggman's machines, Black Bull or G.U.N. Robots but in Knuckles the hero story bosses are Chaos evolving from absorbing chaos Emeralds(Chaos 2,3 and 4), the Dark story bosses are still Heavy Dog or Blue Falcon but also Tikal reserects Echidnas from her tribe to defeat you because she sees you as a threat, the final bosses instead of Black Doom is Chaos 5, instead of Sonic and Diablon is Tikal and her Father Pachacmac, and the Egg-Dealer remains
Instead of Black Arms and G.U.N. Soldiers, the enemies will include Chaos telling you to kill your fellow Echidnas and Tikal telling you to destroy the Artifical Chaos built by Dr. Gerald Robotnik
Previously, Shadow uses Chaos Control and Chaos Blast with full gauges but Knuckles uses these: With a full Hero Gauge you jump 2 metres in the air and glow blue, then bright green rain falls from the sky healing you and anyone within 20 metres, With a full Dark Gauge you slam your fists into the ground and glow red, then these bright orange rocks fall from the sky reigning terror and destruction within 20 metres, You can still use Melee combat and the homing attack aswell
After unlocking every stage and beating every boss you unlock the Last Story Mode, in Shadow you turn into Super Shadow and fight Devil Doom over Earth as it is covered in gas, but here You use the Master Emerald to to turn into Super Knuckles and Fight Perfect Chaos, after which you Trap him inside the Master Emerald along with Tikal, Never to be seen again...The End?