Successfully complete the game on Perfect Agent mode to unlock Dark Agent mode.

 X-ray goggles and Hawk in Mission 7

At the beginning of Mission 7, before or after you kill the two brothers, there are four lockers on the right wall of the side of the bridge that you start at. If you are looking directly across the bridge and turn 90 degrees, you will see four lockers on the wall. In one of them is a pair of X-ray goggles. If you look around in the wooden crates on the side that you started on, there should be a new weapon called the Hawk. It is a disk that you can throw and slice people with.

Secret passage in Mission 7

Before Mission 7, select the demolition kit from the weapons menu. During the mission, after you kill the two brothers go across the bridge towards the rocket. When you get to the rocket, go left and down that road. When you get to the end of the road, there should be two doors (one on the left and another on the right). If you try to open them, they will say "secured". If you go on to a ramp that is on the right side of the left door, there will be a crack in the wall. Use the demolition kit to blow up the crack to get into the door.

Dodging the final Boss' moves in Mission 13

When the final Boss shoots plasma balls at you, just move out of the way. When he teleports onto your platform and starts running at you with the sword, just dive roll out of the way immediately before he swings the sword. This will save you from taking a lot of damage.

Defeating the final Boss in Mission 13