Team Sonic makes an appearance in Sonic Heroes 2. In this game, it contains Sonic, Shadow, Silver and Scourge. Each has its own location; Sonic uses Green Hill Zone, Shadow uses Emerald Hill Zone, Silver uses Great Turquoise Zone and Scourge uses Mecha Green Hill Zone prior to ousting Team Covert from the Underground base and the underground base following their discommunication.
The storyline does involve defeating Dr. Eggman, but not exclusively. As a 'warm-up', Team Sonic have to boot Team Covert out of the Underground base after Manic and Sonia complain of a racket in Gigalopolis.
At the end of HydroCity, we see a cutscene where Knuckles runs straight into Shadow. This is the first SSS have heard of Knuckles and Shade, so they try to quiz him on it with little success; Knuckles is too scared to be able to talk about anything other than Scourge having smashed the Master Emerald, him running off to Great Turquoise Zone and Knuckles wanting SSS to have a word with him, which they happily oblige to do. Sunset Park Zone plays.
When they reach Great Turquoise Zone, with an angry Shadow waiting to teach Scourge a lesson his way, they actually find Scourge shaking. Coldness, Sonic assumes. How wrong could he get. Scourge hadn't smashed the Emerald, oh no. He was sneaking up on it to nick it at the same time Team Eggman attacked it, causing him to get blamed for it being smashed. Sonic calms down Scourge and brings him back to Green Hill Zone.
The cutscene showing SSSS walking from Great Turquoise Zone down to Green Hill Zone is omitted. We catch the end of it before they find Team Babylon waiting for them, blaming them for their parts being missing. Racecourse Resort Island plays; after the race ends, all eight characters are still racing. It takes the distraction of Storm the Albatross by Wave the Swallow to bring them down. They storm off back to Scrap Brain Zone.
For a while, they relax. Perhaps a while short enough that it competes with the very definition of the word; Manic and Sonia come running down complaining of a racket coming from Gigalopolis. With nothing better to do and having not fully chilled down from their Babylonian antics, decide to take a look - except they have no idea how to get there. What we next see is SSSS and M&S on the Mystic Ruins North/Gigalopolis border, with M&S explaining that it went 'down there'. Action stages Gigalopolis and Sleeping Egg Zone are played.
After Sleeping Egg, Mecha Green Hill Zone doesn't begin immediately. There is a small cutscene where Sonic and Scourge enter an argument; Sonic used to spend many hours in this base assisting Dr. Kintobor, and so to him the base's state is appalling. Scourge, on the other hand, finds its presentation quite acceptable and so the two of them lock horns with each other for a bit until Shadow spots something that may be of interest.
Footprints leading all the way from here downwards, in the general direction that SSSS were actually travelling. From here, Mecha Green Hill Zone acts one and two and Electric Egg Zone are played. It's at the end of this that their first taste of the damage inflicted is made evident; they reach the end of the underground zone, and encounter a load of copper piping. They decide to spin dash their way down there; not the wisest of moves, as it causes them to get very dizzy indeed from banging all around the edges of the tubing. Action stage Crystal Egg Zone plays; it's a shorter version than usual, but you play it with a twist; you cannot walk in a completely straight line from disorientation. At the end of it, the disorientation disappears and Scrambled Egg Zone is played in its entirety.
Once at the end of it, they encounter a less-than-content Team Rose, who from their Eggmaniac antics and interruption by Team Dark and Team Badnik are rather irascible. After perhaps not the easiest conversation engaged in, they walk out; the cutscene skips to the Mystic Ruins North/Underground border, where without assistance they don't have much hope of being able to walk straight to them. So they leave it up to you; action stage Underground Zone is played. Once it's over, they fulfill their promise to Team Underground.
On their way out, they spot something very odd; something very loud coming from near Emerald Hill Zone. They look up, and Sonic groans - the Egg Carrier, as big and bellicose as ever. SSSS looks at each other in a circular motion. After some desperate looks and some baffled questioning, they decide that the best thing to do is to find a high point. Gimmick Mountain Zone was best for this job. So they bolted. Fortunately, the Egg Carrier was passing that way, so actually, it was just a simple case of jumping on. SSS were incredibly grateful that Scourge is capable of all three of them, and like monkeys, they jumped and landed. Flying Battery Zone begins.
Their relief to be away from the engines was short-lived. They came face-to-face with Chaos Emerl 6. A boss fight against them ensues. After he is disposed of, the engine starts to lose altitude. Tails sees SSSS and offers a ride; when they get back to where it was parked, Chaos Emerl had already got there first, and had nicked the Emerald from it. The result? Perfect Chaos Emerl. What little the Carrier had left in it (by this point the flames in the engine room were powering it exactly) was promptly zeroed. The result? The Carrier began to spin out, causing it to land in the volcano.
The final scene sees SSSS walking, as dazed as after going for a ride down the copper tubing chute, walk slowly away from the wreckage and speak slurredly for a while, after which they sober up and bid each other a temporary goodbye; they then go to their respective locations.