In N.E.O, secrets have form of black briefcases. You can get them for successfully completing a bonus mission or find lying somewhere on the level. And below is the list of every unlockable bonuses you can find in the game.

Secret combos and special combos:
- "Code Breaker" - "Weapon(NEO Online Gold) Training" mission.
- "Quick Kicks" - "Storming the Drain" mission.
- "Machine Gun Kick" - "The Chase", I Need an Exit mission.
- "Ultimate Hyper Strike" - "Red Pill Rescue": Security Guard mission.
- "The Beginning of the End" Seraph's Apology mission.
- "The One" - "The Burly Braw" mission.

Media Viewer materials:
- "Level Concepts" - "They're Coming for you", Neo mission.
- "Character Concepts (part 1)" - we get this after completing the "Dojo Training" mission.
- "Character Concepts (part 2)" - "Taking the floor" mission.
- "Level Studies" - "Captains Rescue" - "Morpheus and Trinity" mission.
- "Renderings (part 1)" - "Downside Up" mission.
- "Renderings (part 2)" - "Ministry Of Smith's" mission.
- "Art Graveyard" - "Helicopter Rescue" mission.