Launch Base Zone features a gauntlet of bosses, culminating in the final confrontation with Dr. Robotnik and his ultimate weapon, Big Arm.

Mini-Boss: Laser Mobile
- Location: Launch Base Zone Act 1
- Description: A large robot that fires powerful lasers.
- Attack Pattern: Moves back and forth, occasionally stopping to fire powerful lasers horizontally.
- Strategy: Attack the Laser Mobile when it's not firing. Wait for it to finish its laser attack, then jump and hit its cockpit. Be careful of the lasers, as they can be difficult to avoid in the confined space. Three to four hits will destroy it. The Flame Shield's double jump can help you reach its cockpit more easily.
- Weakness: Cockpit when not firing.
- Reward: Clear path to the next section.
Mini-Boss 1: Big Icedrop
- Location: Launch Base Zone Act 2 (First Boss)
- Description: A large, spiked ball that drops from the ceiling.
- Attack Pattern: Drops from the ceiling and bounces erratically around the arena.
- Strategy: Attack the Big Icedrop when it's not bouncing. Wait for it to settle, then jump and hit its top. Be careful of its erratic bouncing pattern, as it can be unpredictable. Three to four hits will destroy it.
- Weakness: Top when settled.
- Reward: Progress to the next boss.
Mini-Boss 2: Red Eye
- Location: Launch Base Zone Act 2 (Second Boss)
- Description: A large, stationary robot with a single eye that fires lasers.
- Attack Pattern: Remains stationary, periodically opening its eye to fire lasers.
- Strategy: Attack the Red Eye when its eye is open. Wait for it to open its eye, then jump and hit it. Be careful of the lasers it fires, as they can be difficult to avoid. Three to four hits will destroy it.
- Weakness: Eye when open.
- Reward: Progress to the final boss.
Final Boss: Big Arm
- Location: Launch Base Zone Act 2 (Final Boss)
- Description: Dr. Robotnik's ultimate weapon, a large robot with two massive arms.
- Attack Pattern: Uses its arms to smash the ground, creating shockwaves, and attempts to grab you.
- Strategy: The arena is small, making evasion difficult. The key is to attack its head when its arms are retracted or after it has performed an attack. When it smashes its arms, jump over them. When it tries to grab you, quickly jump or Spin Dash away. Use the Spin Dash to quickly get into position for an attack. Seven to eight hits will defeat Big Arm.
- Weakness: Robotnik's cockpit/head.
- Reward: Completion of Sonic the Hedgehog 3.