The first of the 'Pure Dark' levels, Central City is only accessible by taking the evil route in Cryptic Castle (which involves fighting against the Black Arms by helping Eggman defend his fortress). Nonetheless, Shadow's general behavior up to now seems to have satisfied Black Doom as to his loyalties. Before the level begins, the alien leader tells Shadow that his past is "filled with hatred and contempt for the humans", and that he should take revenge on them with his own two hands. To this end, the hedgehog is told to detonate five giant bombs which the Arms have set around the city.
Standing in the Arms' way is also Knuckles the Echidna, helping out the human defenders as he did in Glyphic Canyon. Knuckles asks Shadow to help in defusing twenty smaller bombs, which can be accomplished by grabbing a vacuum gun (or Vacuum Egg from a special crate) and sucking the devices up harmlessly. It is unknown if the events associated with Central City took place or not. The President has received a call from the Secretary that the Black Arms are invading Central City. The next scene shows Shadow with the Black Arms aliens behind him. Black Doom proceeds to tell him that the humans took their revenge on him and now he must punish them. Afterward you proceed through the level and get ready to do either the hero or dark mission. If the player does Knuckles' hero mission, the city will be saved, but if he/she does Black Doom's mission, the city will be destroyed.
- Hang onto the bottom of the helicopter, and jump off when it rises high enough for you to jump to the roof. Defeat the Black Arms Soldiers, and the key in the locked box will be yours.
- Next to the Third Checkpoint is a near unbreakable substance. You can breack it by using the Chaos Blast.
- After the fourth Checkpoint, defeat the Black Arms Soldiers and Wings to unlock the spring. Use the spring to launch up to the ledge with the small bombs. Jump over to the ledge with the key after that.
- Located nest to the fifth giant bomb located in a locked box. You must defeat the GUN Beetles to unlock it.
- After the Sixth Checkpoint, destroy one of the building's walls to reveal the key behind it. The wall you need to destroy will be on the left side, If you are moving forward through the stage. You will need a bazooka-Type weapon or a bomb in order to destroy the wall.
Set off the giant bomb!
- Guide: Doom's Eye
- Objective: Detonate the five giant bombs in the city.
- Tips: Attack each bomb to detonate it. The first bomb is close to checkpoint #1. The second is after a triangle jumping area on the roof. The third is in a cage close to checkpoint #3. The fourth is locked in a cage in the toxic waste area. After getting past the toxic waste area, destroy some nearby debris to reveal a spring. Jump on the spring and you will find the bomb in a cage. Each cage can be opened by defeating the nearby GUN troops.
- Some of the bombs can be destroyed with Chaos Blast.
|A||≥ 28,000 points|
|E||< 12,000 points|
Leads to: The ARK
Dispose of the small bombs!
- Guide: Knuckles
- Objective: Dispose of the 20 small bombs in the city.
- Tips: The Vacuum Pod weapon is the only way to properly dispose of the bombs. Shortly past where you meet with Knuckles is a Black Arms soldier that holds this weapon.
Unlike in the Dark mission, you will need to stay in the bottom section of the map to find the small bombs.
|A||≥ 18,000 points|
|E||< 12,000 points|
Leads to: Air Fleet
Behind the Secret Door
A Black Arms' Air Saucer is behind a secret door. The Black Arms' Air Saucer is used to cross poisonous liquid
- This stage is actually a modified version of the Westopolis stage, but at a slightly different time and with some new areas.
- Since both missions are non-linear and there are multiple paths throughout, this is the only stage in Shadow the Hedgehog that doesn't have a Goal Ring.
- As such, this is another stage that doesn't have a Neutral mission.
- Due to the lack of a Goal Ring, during Expert Mode you must activate the large bombs. It is one of three stages in Expert Mode where this happens.
- This level's dark mission arose much controversy regarding the 7/7 London attacks as this game was released not long after the attacks which one involved detonating bombs. The victims of the 7/7 London attacks especially claimed that this mission was a re-enactment of the events.