Here's the location of the Secret Items.
1 Destroy plus escapee: On a ledge of the building about 3 levels down.
2 Guard wharf warehouse: Turn around at the start and steal the radar you are guarding.
3 Destroy fuel depot: In the 2nd room on the shelf at the back, destroy the fuel canisters, then go up there and search the rear corner.
4 Retake air cleaner: Inside a grate on the ceiling.
5 Kill struggle leader: At the bottom of the area where the floor explodes, search the rear of the floor of the chasm.
6 Exterminate organisms: Search the rear of the queen's chamber.
7 Guard freight train: Destroy one of the boxes at the loading area.
8 Destroy intruders: In a niche under the topmost bridge.
9 Guard factory entrance: In a "RED" corner of the map.
10 Secret factory recon: In a "RED" corner of the map.
11 Eliminate strikers: At the start, turn around and destroy one of the armored cars.