1- the first secret mission is on mission 3 you gotta drop into the water near the broken bridge (gotta drop down there yourself wont count if you go with the 1 they drop you in there for)

2- 2nd secret mission is on mission 4 when you battle phantom (lava spider looking boss) you gotta go back into the room

3- 3rd is on mission 4 also. complete secret mission 2 and a door will show up called the god of times room. go in there.

4-4th is also on mission 4. in the god of times room its under the biplane door

5- 5th is on mission 5. simply go back to the room where you saw the beezelbub.

6- 6th is on mission 11. go back threw the door that ended mission 10

7- 7th is on mission 13. there is a room with the captains skeleton. go to it

8- 8th is on mission 15. look at the skull in the room where you found the shield emblem

9- 9th is on mission 16. beat griffion (giant bird) then go back to the collisiem

10- 10th is on mission 16 also beat nightmare and enter the biplane room again

11- 11th is on mission 17. cross the broken bridge. (i used air raid)

12- the final secret mission is on mission 21. look at the wall infront of the god of time statue.

hope this walkthrough helped. tried to leave as many spoilers out as possible. so need more help msg me