Their storyline is a take on about the most abused storyline in the entire of the Sonic series; the Master Emerald has been shattered, and Knuckles goes in search for the pieces. Only this time, not only is he doing so whilst infatuated with Shade but also in Shade's company and in Mighty's and Ray's.
Knuckles is sleeping on the path of the Master Emerald whilst with Shade, when suddenly the Emerald is busted, Chaos released, the Egg Carrier behind them, accelerating away and Scourge running away from Angel Island; an incensed Knuckles bolts out of Angel Island; we next see him in Mystic Ruins South. Note that between these two destinations is the encounter of Knuckles and SSS colliding with each other; we don't actually see that in this storyline, theirs only. The cut-scene restarts with Knuckles having ran so far he has ran out of breath; while Shade has plenty of energy left, Knuckles is exhausted. Shade plays the zone Mystic Ruins (the entire of) on her own. After this, we see a cutscene in which Mighty and Ray encounter the debilitated Knuckles and have a chat, after which Shade turns up to check on Knuckles, berates him for deeming his mothers' meetings more important than the Master Emerald, and presents her shards. Realizing that the four of them possess a shared aim, they decide to team up. Their next destination is Green Hill Zone; at the end of this, they encounter Team Babylon. They don't fight - yet - as it is not Team Knuckles they are in a bad mood with, but reminder of who started this prompts Knuckles to return to Great Turquoise Zone in the hope of finding Scourge; the search only yields more Emerald shards.
Whilst there, Knuckles realizes something. Some of the pieces have, by freak nature, remained in Angel Island and some have flown into Sandopolis. And he realizes that some have been spewed into Reactive Factory Zone. At this point, the team splits into two (perhaps obviously, Knuckles and Shade/Mighty and Ray), with the former attending to Angel Island and Sandopolis and the latter dealing with Reactive Factory.
|Mighty/Ray||Reactive Factory Zone|
After this, the game zooms into a cut-scene where Knuckles and Shade are 'seeing' into the Master Emerald, like Knuckles does on his own in Sonic Adventure. From here, we are taken from Angel Island to Station Square, remaining as Knuckles and Shade, and we hear an extended mother's meeting until Mighty and Ray arrive. They then try to make their own way back to Angel Island, picking up the penultimate set of Emerald shards as they go (zone Oil Ocean is played; this involves an extended action stage through Oil Ocean and then a treasure-hunting stage in Aquatic Mine. This is in the same style as Big's Hot Shelter in Sonic Adventure, though with a lot more action stage than Hot Shelter!). This is impossible, however; since their last attendance at Casinopolis (which they passed now and before) a whacking great commotion has ensued. Chaos Emerl 4 and Team Eggman have appeared out of nowhere and are causing commotion left, right and center. However, the Egg Carrier, with Team Eggman causing commotion here, has been
parked left unattended in Aquatic Ruin Zone, so the team simply sneak on board (there is an empty compartment in an isolated part of the Carrier) and wait for Team Eggman to re-attend.
Next, while Team Eggman are busy circumnavigating the place, Team Knuckles are to complete Sky Deck Zone, the final set of Emerald shards, but with a twist; you must NOT be detected by man or beast else they will scream and you will be booted out of the zone. Once done, you will land up in the engine room of the Carrier. It is here Chaos Emerl 6, by this point a room-sized monster damageable only by detonating the engines of the Carrier in front of him, is fought. Once done, even though the Carrier descends quite rapidly in a northbound direction; this causes no hassle for any of the team (as Echidnas, both Knuckles and Shade have the ability to drift, Ray can fly and Mighty lies on Knuckles' back). They land on Angel Island, deposit their shards and celebrate a joyous moment. However, this moment is interrupted by the Egg Carrier - or at least its carcass - landing head first into the head of the volcano.