Sonic 3 & Knuckles is a combination game, playable when the cartridge for Sonic the Hedgehog 3 is inserted into the lock-on cartridge for Sonic & Knuckles. In truth, Sonic 3 & Knuckles is the true "Sonic 3", but was separated into two games due to time constraints and cartridge prices. Within this game, the player can control Knuckles in the Sonic 3 stages and Tails in the Sonic & Knuckles stages. Also, after collecting all seven Chaos Emeralds, the player can collect the Super Emeralds to achieve a Hyper form (Super form for Tails).
Sonic the Hedgehog and Miles "Tails" Prower
In Sonic's story (following the events of Sonic The Hedgehog 2), Sonic finds Angel Island, jumps off the Tornado and turns Super Sonic as he arrives on the Island. Once there, Knuckles the Echidna, the Island's guardian, surprises the blue hedgehog and causes Sonic to lose his Super form. While Sonic is still dazed, Knuckles steals the Emeralds and hides them in the Special Stage. While running through Angel Island Zone, Sonic and Tails encounter a Fire Breath and an army of them which burn Angel Island Zone. Soon, Sonic and Tails are running away from a flying fortress and encounters Robotnik in his Flame Mobile. After the humiliating defeat, Robotnik retreats and leaves behind an Egg Capsule. Knuckles then appears and destroys the bridge Sonic and Tails are on, sending them into Hydrocity Zone.
After falling into Hydrocity Zone, Sonic and Tails navigate through the ancient waterways and encounter the Big Shaker robot, which Sonic and Tails were able to swiftly defeat. Near the end of Act 2, the duo encounters Knuckles again, who drops them into an area where Robotnik is waiting with his Screw Mobile. After freeing the animals, Sonic and Tails are blasted into Marble Garden Zone.
While in Marble Garden Zone, Sonic and Tails enter the last of the Special Stages and acquire the last Chaos Emerald. At various points, Sonic and Tails spot the Tunnelbot, which drills into the Zone. At the end of Act 1, Sonic and Tails battle the Tunnelbot and proceeds to Act 2. In Act 2, Robotnik appears to try to stop Sonic and Tails by causing the Zone to deteriorate, threatening to squash the duo. In the end, Robotnik finally encounters Sonic and Tails, and destroys the platform he was standing on with his Drill Mobile and Sonic is forced to fight Robotnik in the air with Tails keeping him in the air. Should Sonic fall, Tails will fly down and catch Sonic. Afterwards, Sonic and Tails try to find a place to land and end up in Carnival Night Zone.
In Carnival Night Zone, the pair encounter many gimmicks such as tunnels that instantly speed them up. After running through the casino-like stage, Sonic and Tails fight the Bowling Spin robot, which can only be damaged by hitting it's body and the top has to hit it's vulnerable body. Halfway through Act 2, Sonic and Tails meets Knuckles again, who presses a switch causing the power to go out and the water to go up. After restoring the power, Sonic and Tails spot Knuckles again who activates another switch which takes them to Robotnik in his Graviton Mobile, which will drop a metal ball and Robotnik will use a kind of electric suction. But he has to drop down to collect the ball the repeat the attack. After the boss fight, Sonic gets into a cannon which launches him to Ice Cap Zone.
After snowboarding in Ice Cap Zone, Sonic hits a wall and snow falls on him. At the end, Sonic and Tails encounter Big Icedus which was swiftly destroyed as well, and during Act 2, Sonic spends most of the level above ground. Near the end, Sonic gains enough speed to get to a secret area with many rings and a Giant Ring. The boss for this stage is, once again, Robotnik in his Freezer Mobile. After the victory, Sonic and Tails spin dash into Launch Base Zone.
In Launch Base Zone, Robotnik has taken all precautions to stop the heroic duo and fix the Death Egg. He even pitted them against his newest robot, the Twin Hammer. Sonic and Tails then race to the end to finish the job against Robotnik, who was revealed to have been waiting for them and uses the Ball Shooter to try to stop them, but all in vain. When the mad scientist runs away, he leaves behind an Egg Mobile which Sonic and Tails use to chase after him. But along the way, they encounter Knuckles again who prevents them from proceeding. But when the Death Egg starts to launch, Knuckles falls off and Sonic and Tails continue to a small platform to fight Robotnik one last time. The Mobile he uses is called the Beam Rocket which is just a tall Mobile that fires lasers but it has a small orb that circles the cockpit to protect it from attacks. After the battle, Sonic and Tails watch as the Death Egg falls into a volcano,while Sonic and Tails land in a stage filled with large mushrooms.
Tails flies Sonic down to Mushroom Hill Zone, but Knuckles was there too. They saw him leaving a room, as if trying to keep a secret. When he leaves, the two see what he is trying to hide, which was revealed to be another Giant Ring but sends them to the Master Emerald where the Chaos Emeralds react to the Master Emerald, turning them into grey Super Emeralds, in which Sonic has to step on them to activate Special Stages to get the Super Emeralds. After clearing the Special Stage, Sonic and Tails continue through Mushroom Hill Zone, and discovers the Hey Ho which cuts down trees to attack Sonic. After winning against the robot, Sonic and Tails spot Knuckles who sends them into the utmost part of Mushroom Hill. Along the way to the end, Sonic finds more Giant Rings and obtains more Super Emeralds. At the end, Sonic and Tails discover Robotnik is still alive and is sending some kind of transmission. After disrupting the signal, Robotnik tries to escape but Sonic and Tails are able to stop him and see Robotnik escape to a flying fortress.
In Flying Battery Zone, Sonic and Tails have to be very careful, as one false step could be their last, since they are very high above the ground. With Sonic finding more Super Emeralds, the Special Stages were getting harder and harder. At the very end of Act 1, Sonic and Tails thought they got a break and didn't have to fight a boss and just destroy the Egg Capsule. But when they jumped on it, the Sub-boss revealed himself as the Gapsule. All Sonic and Tails have to do is stand in the very top and quickly move when one of the arms are coming down. After the boss is defeated, small animals are released and Sonic and Tails continue on their way. Before reaching Robotnik, Sonic gets the last of the Super Emeralds and is able to transform into Hyper Sonic. When he finds Robotnik, he traps Sonic and Tails by two barriers known as the Barrier Eggman (much like the boss for Wing Fortress Zone in Sonic the Hedgehog 2) and after a while, Robotnik's control panel will explode and he'll run away with Sonic following close behind. Robotnik then ambushes Sonic and Tails with the Hang Mobile which Sonic and Tails were able to defeat when Robotnik spun around. Sonic and Tails then ran after Robotnik who escaped to Sandopolis Zone.
Once Sonic and Tails reach Sandopolis Zone, they discover that Robotnik's influence has reached this area too. And the also used the climbing sand to reach new places and reach the end. Finally, they reach a small piece of solid ground, but suddenly, a huge pyramid rises up and a huge stone golem appears in the entrance. After Sonic and Tails push it into the quicksand, the duo enters the pyramid. Inside the pyramid, Sonic accidentally opens a capsule that releases a few ghosts. They hate the light and attack Sonic and Tails when the lights are off. The two also discover an endless sand slide, but Sonic and Tails find their way out by jumping onto a moving platform they found while sliding. They finally finds Robotnik in his new Egg Golem. If Sonic and Tails were to fail to defeat it in enough time, they would get squashed against the Egg Golem and the opposite wall. After beating the Egg Golem, the blue hedgehog and his young friend fall into the inside of a volcano.
Inside Lava Reef Zone, Sonic and Tails discovered that now Robotnik is even more determined to kill the blue hedgehog and two-tailed fox. Even creating a robot known as the Lava Drill but it failed to kill Sonic and Tails and was destroyed in the lava. Sonic and Tails later progressed to the Sub-boss of the area, known as Heat Arms, which they defeat. As the bot was blowing up, the lava began to cool down and harden, and the pair later discovered the Death Egg landed on top of Lava Reef, but then Knuckles appeared again and pushed a huge rock, which sent Sonic and Tails into the very bowels of Lava Reef Zone, where Robotnik was once again waiting and fired rockets to destroy the platforms so Sonic and Tails would fall into the lava. After dodging the rockets, the duo fought Robotnik and destroyed his new mech, the Hot Mobile, by waiting for the spiked balls Robotnik fired at them to hit Robotnik. Sonic and Tails then moved on to a palace hidden by the lava.
In Hidden Palace Zone, Sonic and Tails finally met Knuckles face to face, after looking up at the mural on the wall that depicted Sonic fighting Robotnik in space, and enter a stressful fight with Knuckles. During the fight, Robotnik used that time to steal the Master Emerald. After the fight, Knuckles sensed something was wrong with the Master Emerald and ran to see what was the matter. He then discovered that Robotnik played him for a sap and revealed his true intentions rather blatantly (by electrocuting Knuckles) Knuckles then came to and helped Sonic and Tails by showing them a secret passage to a haven in the sky.
In Sky Sanctuary Zone, Sonic and Tails witness the rise of the Death Egg. Knuckles then jumps across a gap to activate a bridge so Sonic and Tails to get across. They wanted Knuckles to come, but Knuckles simply waved them away and was too weak from the fight and "shocking" discovery. Sonic and Tails then proceeded through Sky Sanctuary, eventually, coming across Mecha Sonic who fought them three times (twice in the Egg Mobile, once on foot), the first time was in the Egg Mobile with the wrecking ball (much like the famous boss from Green Hill Zone in the first game), the Egg Mobile with smaller clones (the boss from Metropolis Zone in Sonic the Hedgehog 2), and finally fought Sonic and Tails on foot which Sonic and Tails emerged victorious. But then the platform began to fall so they jumped onto a large pillar which they were able to use to get to the Death Egg Zone.
In the Death Egg Zone, Robotnik is pulling out all the tricks and traps to stop Sonic and Tails, but the duo are able to avoid the traps and reach the Sub-boss, Red Eye. After Sonic and Tails defeated the machine, they travel deeper into the Death Egg. Soon, Sonic and Tails corner Robotnik but the Dr. turns the tides and unleashes his newest robot, the Death Ball. After causing the spiked rollers to hit the underside of the Death Ball, Robotnik runs away with Sonic and Tails hot on his trail. The mad doctor jumps in a giant robot that looks just like Robotnik. He mainly attacks Sonic and Tails by slamming it's fingers down. After those are destroyed, Robotnik slowly destroys the stage from the left. He will breath fire at Sonic and Tails through it's nose. When Sonic and Tails dodge the flames, the generator holding the Master Emerald appears. Sonic and Tails attack it as much as they can before it fires a huge laser. After repeating the process, the giant robot falls and is destroyed but Robotnik isn't ready to give up. He escapes the wreckage in his Egg Mobile with the Master Emerald in tow. After a while, Robotnik is forced to drop the Master Emerald, but steals it back. Sonic, using the power of the Chaos Emeralds (or Super Emeralds), transforms into Super Sonic (or Hyper Sonic) to get back the Master Emerald, thus leading to the final Zone.
In the Doomsday Zone, Sonic, using the power of either the seven Chaos or Super Emeralds, transforms into Super Sonic or Hyper Sonic to take the Master Emerald from Robotnik. After collecting rings and dodging asteroids along the way, he meets up with the doctor in his new ship, the Egg Missile. Sonic just has to dodge the small projectiles and get the rockets to hit the head 8 times. After 8 hits, the ship will explode but Robotnik will escape in the Egg Bomber. Sonic pursues Robotnik and dashes into the Egg Bomber until it explodes. Sonic quickly grabs the Master Emerald and falls back to Earth. Tails, who had flown back to Earth to pilot the Tornado, appears and uses a magnetic claw to grab the Master Emerald and they both head back to Angel Island and put the Emerald back on the Island, restoring Angel Island's ability of flight. Sonic and Tails then fly away in the Tornado while Knuckles watches them disappear in the distance, heading towards their next adventure...
Miles "Tails" Prower
Tails starts off in Angel Island Zone, trying to find Knuckles and stop Robotnik. After exploring the Zone, he encounters an army of Fire Breaths which burn Angel Island Zone. Tails journeys through Angel Island, and gets the Chaos Emeralds, and gets into Mushroom Hill Zone and begins to get the Super Emeralds and (finally) is able to transform into Super Tails and stop Robotnik and return the Master Emerald to Knuckles.
Knuckles the Echidna
Knuckles' story takes place after Sonic's story. After the Death Egg crashes on Angel Island for the second time at the hands of Sonic, Robotnik begins to proceed with rebuilding the Death Egg. Feeling Knuckles has served his purpose, he sends EggRobo to eliminate this potential threat. EggRobo finds Knuckles relaxing in Mushroom Hill Zone - and attempts to eliminate him with a bomb - but Knuckles, whether through luck or toughness, survives the attack. Enraged, the wild Echidna sets off to defeat EggRobo. After progressing through the Floating Island in the same order as Sonic, he is taken by EggRobo to Sky Sanctuary. Mecha Sonic then accidentally attacks the EggRobo and fights Knuckles. After losing to the echidna, Mecha Sonic flees and absorbs the power of the Master Emerald and becomes Super Mecha Sonic. Knuckles defeats him nonetheless, and the platform Knuckles was on gives way and luckily, Sonic saves him and takes him back to Angel Island where it's power is fully restored, once again..