This page is split into two games - Sonic the Hedgehog 3 and Sonic & Knuckles.
Meanwhile, the island's guardian, Knuckles the Echidna, is taking his usual walk along the Emerald altar to check if the Emeralds are alright. Then, a huge earthquake came out of nowhere. Knuckles saw the Emeralds reverberating in mid-air - stunned, he was suddenly threw into the air before blacking out. When he woke up, the Chaos Emeralds were gone, but Knuckles also saw a huge egg in the distance. He then recalled a legend of an ancient dragon sent to destroy the world in the end times; thinking this mysterious egg to be the dragon he set out towards it.
Just then, a giant egg-shaped figure appeared out of nowhere, calling himself "Dr. Robotnik". He explained to Knuckles he had come here to study this giant egg, and that an evil hedgehog named Sonic was not only interfering with his research, but planned to steal the Chaos Emeralds as well. Knuckles, duped by the doctor, ran off to find this miscreant. Eggman smiled at himself, pleased at his ability to lie.
According to the Japanese manual (which was adapted into the PC version's help file), Sonic and Tails resumed taking a break on an island some distance away. Tails detects a strong Chaos Emerald reading with his invention, the Jewel Radar. Thinking that it had to do with the sudden tidal wave that occurred after the Death Egg's defeat, he decides to consult with Sonic to investigate. Meanwhile, Sonic woke up from his nap on the beach to find a Ring engraved with ancient letters washed ashore, which reminded him of a legend - an ancient civilization once tried to take a prosperous stone for its power, but were wiped out in an instant. It is said that the kami descended from the sky and reshaped their territory as an isolated floating island, along with the mighty stone of power. With a renewed sense of adventure, Sonic joined Tails to take the Tornado to the ocean. These details are not mentioned in most releases of the game.
They find the landmass previously known as the Floating Island resting on the ocean. Excited, Sonic hops off the Tornado prematurely and uses the power of the Chaos Emeralds he found during his previous adventure to transform into Super Sonic, showing off as he races the Tornado by gliding across the surface of the water. Unfortunately, he is caught off guard with the spiked glove of an echidna named Knuckles. Knuckles, as we know, was tricked by Dr. Robotnik into thinking that Sonic and Tails are thieves, so he quickly took Sonic's own Emeralds and hid them. Tails soon joined Sonic and they set off to explore and stop the nefarious Dr. Robotnik's plans while evading Knuckles' cunning traps.
When Sonic and Tails reached Robotnik's Launch Base, they made their way to the crashed Death Egg, hoping to stop its launch. Though Robotnik manages to briefly get the Death Egg flying without the Chaos Emeralds, he and his mechs were defeated by Sonic and Tails, and soon after the Death Egg stopped functioning and fell again.
In the underground Hidden Palace, Dr. Robotnik takes advantage of the confusion between Sonic and Knuckles in order to obtain the Master Emerald. Knuckles then realizes that Dr. Robotnik has been tricking him all along, and he is electrocuted while trying to stop Robotnik from stealing the Emerald. Knuckles helps Sonic to get to Sky Sanctuary, then leaves him to defeat Robotnik and trusts him to return the Master Emerald. Sonic takes on the Death Egg and defeats Robotnik's escape mech to bring back the Master Emerald, making the Floating Island regain its namesake. However, a lone Eggrobo takes up the Doctor's mantle. (Note that Tails accompanies Sonic during his adventure up until The Doomsday Zone in the complete Sonic 3 & Knuckles - otherwise, he is only seen piloting the Tornado in Sonic's ending.)
Soon after this event, Knuckles is seen relaxing with the Animals in Mushroom Hill. Suddenly, the remaining Eggrobo throws a bomb. Knuckles becomes angry at the Eggrobo and chases after him, starting Knuckles' storyline in the game. (Note that this event only takes place in the standalone Sonic & Knuckles - in the full game, he begins at Angel Island Zone without this intro.) As Knuckles races through the zones, Knuckles accesses new places Sonic could not. After Knuckles exits Hidden Palace through the teleporter, the Eggrobo grabs Knuckles and is faced with Mecha Sonic. Knuckles glides out of the way as Mecha Sonic destroys the Eggrobo, and the two fight. After defeat, Mecha Sonic dashes to the Master Emerald and uses it to achieve its Super State. Knuckles defeats Mecha Sonic, which makes the platform collapse. However, Sonic arrives with the Tornado, saving Knuckles. Knuckles returns to the Floating Island with the Master Emerald, making it maintain its flight.