In the game, there are some secret missions one can access by meeting certain criteria:
Secret Mission 1: Destruction - In Mission 2: Corrosion, after destroying the first door inside the base, there are five floating towers--the outer four are blue and the center one is red. Shoot the blue towers and then the red one, and you'll open up an underground tunnel that eventually leads to the secret mission.
Secret Mission 2: Scars: - About 1/5 into Mission 3: Invaded, several blue ships line up in front of a single red one. Destroy ONLY the red ship. Rather than enter the space station, you will fly over it and eventually enter the secret mission.
Secret Mission 3: Reminiscence - In Mission 4; Pursuit, after passing by the series of launch bays but before entering the canyon, four blue ships will face you. Eventually, four red ships will line up behind the blue ones. Again, destroy only the red ships, avoiding the blue ones. Done correctly, your ship will change course and travel into a secret section of the canyon where your ship will be teleported to the secret mission.