This is the plot of Eggman's Adventure. It is a detailed description of the entirety of the plot, and as such, there are many spoilers!
Chapter 1 - Green Hill Tooooown, the Marble Ruins, and Scrap Bacon ZoneEdit
Aboard the Death Bacon, Dr. Baconman laughs, claiming to have seized the Chaos Emeralds, using them to power up the space station. He then fires a beam at Eggman's base, where Eggman is waiting, bored. The beam completely obliterates the base, but leaves Eggman unharmed. He deduces that Baconman must be behind the attack, and resolves to stop him. The doctor then heads to Green Hill Town, where he meets Random Wise Man. Random Wise Man tells Eggman that he has an older brother who lives in the Marble Ruins, and knows even more than he does. Hoping to learn from this man, Eggman enters the Marble Ruins.
Eggman finds the ruins infested with Mega Baconbots. After he crosses through the ruins, he finds Random Martial Arts Master in a small room in the back. The confused old man mistakes him for an intruder and attacks him. After Eggman shoots him a few times, Random Martial Arts Master, impressed by Eggman's skill, teaches him the SupaDupaMegaAttack, and tells him to return to Green Hill Town.
Once there, Eggman finds that the town has been invaded by B-1000s. Eggman decides to head for the enemy base, the Scrap Bacon Zone, and fights his way through B-1000s to get there. Once inside, he proceeds through the heavily guarded base, meeting General B-1000. The general threatens to annihilate Eggman, and they do battle. Eggman defeats him handily and retrieves a Chaos Emerald from the Scrap Bacon Zone.
Chapter 2 - The Desert, the Pyramid, and the Oil PlantEdit
Baconman, frustrated by Eggman's victory, shouts at a group of B-1000s. He muses that the nearest Chaos Emerald to Eggman is being held in the desert, and surmises that Eggman will head there next. Saying that they cannot allow Eggman to learn about the Chaos Beam, he sends his B-1000s to the desert to ambush him. Meanwhile, Eggman is, as Baconman guessed, heading to the desert abord a boat. Eggman arrives in the desert after a short trip, and on his way through the town, is ambushed by B-1000s. He defeats them, and they mention that the key to Baconman's Oil Plant is hidden in the Ancient Pyramid. Realizing they've said too much, the B-1000s flee, threatening to return.
Random Wise Man confirms what the B-1000s said, and mentions that a Chaos Emerald is hidden in Baconman's Oil Plant. Eggman heads to the pyramid, finding it filled with Desert Baconbots. As he reaches the back of the pyramid, he finds a switch guarded by Desert Baconbots. Eggman defeats them and pulls the switch, opening the way to Baconman's Oil Plant. The path opened, Eggman heads south to the oil plant.
Eggman heads through the factory, searching for the Chaos Emerald, when at last, he comes upon the central computer of the Baconman Co. Oil Plant. He battles the computer, which attacks using Bacon Beams and viruses. In the end, Eggman is able to defeat the computer, and obtains another Chaos Emerald.
Chapter 3 - Ocean Resort, Jungle, and CasinoEdit
Baconman is frustrated by Eggman's second success, but calms down as he convinces himself that his new ally's project will bring him world domination. He then shouts to get "the creepy old guy with an eccentric fascination with cheese" on the phone. Back on Earth, Eggman is told by Random Wise Man to head for the Ocean Resort. Finding a random gang of pirates, Eggman rents a boat and heads for the Ocean Resort Zone. However, on his way, he is stopped by the Cheese Ship. The Cheese Ship asks if Eggman is Splooshnic, then decides that it doesn't matter either way, and attacks Eggman, shouting that the Cheese Mall will prevail. Eggman defeats the Cheese Ship, which then flees, saying it needs to find the Element Orbs.
Once he arrives at the Ocean Resort, Eggman finds a building with a sign identifying it as Casinopolis. He enters the building, but is told that it's a members only establishment, and as such, he cannot gamble there. Random Wise Man tells Eggman that one of Baconman's bases is hidden underneath the casino, and that he may be able to find a membership card in another nearby ocean resort. Eggman thus heads to a nearby port, where James takes him to the second ocean resort. Once there, Eggman finds a man who tells him that he's lost his wallet in a nearby jungle, and that if Eggman can find it for him, he'll give him a casino membership card.
As Eggman passes through the jungle, he deals with rabid monkeys and a series of obstructions that can only be removed by pulling switches. Eggman locates all of the switches and makes his way to the center of the jungle, where he sees an evil bird holding a wallet. After attacking and defeating the evil bird, Eggman retrieves the wallet and returns it to its owner. Now a member of Casinopolis, Eggman returns to the first ocean resort and heads for Baconman's secret base. As he makes his way through, Eggman finds many of his foes, who remark on his uncanny resemblance to himself.
While searching for the Chaos Emerald, Eggman is stopped by a Baconbot, who wishes to test the new member. The first test he administers is a battle, which Eggman is able to win easilly. Mildly impressed, the Baconbot then quizzes Eggman with trivia. The trivia questions are very Baconman-themed (e.g., "Q: Who's the stupidest person in the entire world? A: Eggman"). Eggman answers the questions, and is informed that Baconman has come to see the new recruit, and is waiting in the next room. As Eggman enters, Baconman is furious that his minions let Eggman in. He then summons his Baconik Slot Machine and leaves for a meeting.
After Eggman destroys the slot machine, he finds a Baconbot who claims to have hidden the Chaos Emerald in the Evil Cheese Shop. Random Wise Man mentions that there is a great evil force that deals in Evil Cheese, and tells Eggman to hurry to the shop. Once there, Eggman finds a tunnel that leads to a mysterious place similar to the Underworld, filled with Improved B-1000s. Using levers, Eggman opens a series of paths until he at last reaches the boss guarding the third Chaos Emerald: Spamman. Claiming that Baconman's paid him a large amount of money to help him establish the Baconman/EWM Co. Cheese-Mall Battlestation, he attacks Eggman. After Eggman beats him, Spamman quits, claiming he hates Baconman even more than he hates Eggman. He then hands the Chaos Emerald over to Eggman.
Chapter 4 - Return to Green Hill Zone, Lake Zone, Mt. Yosh, and the Bacon CarrierEdit
Growing desperate, Baconman reflects on Eggman's continued successes. As he wishes for someone to help him defeat Eggman, the Egg Busters suddenly appear. They inform him of their unorthodox occupation, and agree to hunt down Eggman for him. Unaware of this danger, Eggman has returned to Green Hill Town. There, Random Wise Man tells him that his brother was kidnapped by Baconman, and a tunnel has been found in the Marble Ruins, leading to a mysterious forest. Eggman again heads through the Marble Ruins, now filled with Improved B-1000s, searching for the tunnel. Battling past the B-1000s, Eggman finds the Casino Office Dude waiting for him. He informs Eggman that he lost his job as a result of helping Eggman, and attacks him in a rage. Eggman defeats him and heads onward.
Finding himself in a mysterious forest, Eggman makes his way through the forest. While exploring the forest, he finds Random Wise Man, who tells him that Random Martial Arts Master is being held captive on Mt. Yosh, but that mysterious evil cactuses are blocking the way, and can only be removed with the help of Apple Kid, who lives in Lake Zone City. Eggman tells Random Wise Man that there's a huge rock blocking the way to town, and Random Wise Man claims that he can use his magical powers to remove it. After Eggman leads him to the rock, Random Wise Man uses his magic powers to obliterate it, opening the way to Lake Zone City.
In Lake Zone City, Eggman finds ninjas loitering around, who attack him when he attempts to speak with them. Confused by the presence of the ninjas, Eggman quickly locates Apple Kid. After donating $200 to Apple Kid's research, Eggman is informed that an old man is waiting for him in the pub. Eggman heads to the pub, but is ambushed by the Egg Busters. They attack Eggman with vacuum cleaners, but find them ineffective on the doctor, who makes short work of the Egg Busters. Defeated, the Egg Busters retreat in search of new weapons. Eggman continues on to the pub.
At the pub, Random Wise Man informs Eggman that a powerful item is hidden in a tunnel in the town. As Eggman leaves in search of this item, he is stopped by a Mr. Saturn, who tells him that Apple Kid wishes to speak with him. At the lab, Apple Kid tells Eggman that a special battery can power his newest invention, and, on his way out, Random Wise Man tells him that the tunnel was found near Random Martial Arts Master's dojo. Eggman finds Baconman in the tunnel, setting his mining Sentry Robots to find the battery. Eggman manages to hide from Baconman, and then heads through the tunnel, avoiding the Sentry Robots on the way. At the end of the tunnel, Eggman finds the King of Lake Zone hiding out on a small beach at the base of a cliff. He claims that ninjas ran him out of his home, and gives the battery to Eggman.
After taking the battery to Apple Kid, the cactuses are destroyed, and Eggman climbs Mt. Yosh. On his way to the summit, he is again attacked by the Egg Busters. This time, they attempt to attack him with their bare hands, which goes only marginally better than their vacuum cleaner attempt. After they're defeated, they attempt to teleport away, but after failing repeatedly, they decide to merely retreat. Eggman enters Baconman's hidden base, but there he only finds Super Skyer, who claims that Baconman took the Chaos Emerald away on an airship. Super Skyer then attempts to destroy Eggman, and, though he fails, delays Eggman as Baconman escapes. Not knowing how to get the Emerald now, Eggman leaves the base. As he begins his descent down Mt. Yosh, he is suddenly beamed aboard the Airship.
On the Airship, Banz introduces himself to Eggman, telling him that Baconman is working with Evil Wise Man, and that they plan to combine the power of the Chaos Emeralds and Element Orbs. As the Airship pursues Baconman's Bacon Carrier, Eggman begins to explore, finding the Egg Bazooka. Shortly thereafter, the Airship arrives at the Bacon Carrier, and Eggman boards it. Fighting his way through Yushy B-1000s, Eggman finds Wenk Tnhst. After a brief battle, he defeats the robot and retrieves the fourth Chaos Emerald. However, as he's celebrating, the Egg Busters again attack him. With little effort, Eggman defeats them and heads back to the Airship.
Chapter 4.5 - Loose EndsEdit
After lamenting the weakness of the Egg Busters, Baconman begins a meeting with Evil Wise Man, who is distressed that he is appearing as a silhouette. Baconman tells Evil Wise Man that he will likely be seen in his true form toward the end of the game. He then surmises that Eggman is heading for the Ice Cap Zone, and mentions that there will be a surprise waiting for him there. True to Baconman's prediction, Eggman is headed for the Ice Cap Zone, but Random Wise Man reminds Eggman that his brother is still kidnapped. The Airship immediately returns to Lake Zone City, where Eggman finds Random Martial Arts Master trapped atop a cliff behind the pub. Eggman points out to the old man that he could have merely climbed down the ladder, and returns to the Airship.