Bonuses:
Collect the hidden briefcases to unlock various bonuses. Note: Some briefcases are given as rewards for completing hidden objectives.
The One mode:
Successfully complete the first level Lobby Dreams without dying to unlock The One difficulty setting, which is the hardest difficulty setting.
Defeating Agent Smith:
To defeat Agent Smith at the train station, you must first weaken him. When you hear an announcement of a train approaching, grab a hold of him and throw him in front of the train.
Defeating the Witch:
Use the Bullet Stop ability to throw the various items in the room at her. They each do a lot of damage. When she casts the Barrier spell, avoid her or your weapon will break and you will be stunned. Make sure to disarm her as soon as possible.
Dive through walls in Dojo:
In the Dojo when finding the Killing Blow, you can get through doors easier by diving through them instead of slashing them. You can also tell the difference between fake and real doors by going through them this way.
See through leaves:
In the intermission sequence in the garden, Trinity says "Keep your blade sharp". They turn to face the camera, and you can see Neo's hair through the leaves when they cover his head.
The Code Breaker combo:
Successfully complete all training tutorial objectives to unlock The Code Breaker combo.
The One mode:
Successfully complete the first level Lobby Dreams without dying to unlock the The One difficulty setting, which is the hardest difficulty setting.
Zion Archive level:
Upgrade the icon in the 8 o'clock position on the Atman Principle to permanently unlock the Zion Archive level at the level selection screen.