There are 12 Secret Missions in DMC 3.
SECRET MISSION 1: Mission 3, at the red door right before the golden statue in the right side of 13th Avenue. In this mission, you are transported back to Love Planet.
Objective: In there, you are required to kill all of the enemies in 60 seconds.There are Hell Prides, Hell Lusts, and Hell Sloths here.
SECRET MISSION 2: Mission 5, This one is located beside the large elevator in Mission 5. It is portrayed as a red glowing small object at the wall. By entering this mission, you are now at the Ice Guardian's Chamber.
OBJECTIVE: To complete this mission, you need to kill all four Enigmas without taking any damage. A very good strategy is having a maxed out Trickster Style or Gunslinger Style. It is advised not to use Holy Water since that costs too many Red Orbs.
SECRET MISSION 3: Mission 7, This one can be found right before you enter the first door in Mission 7. It is at the right where there is a ledge above and it is represented as a red glowing candle-like structure.
OBJECTIVE: In this mission, you are required to stay in air for 20 seconds.
SECRET MISSION 4: Mission 8, This one is found in Mission 8 inside the Leviathan's stomach. It is found under the ship behind some wooden planks you have to break. It is portrayed as a large blue glowing tablet. This secret mission has to be accessed and completed before the Ignis Fatuus is obtained, or the tablet will only glow a dull blue in the dark and becomes inaccessible.
OBJECTIVE: In this mission, you are transported back to Surge of Fortunas. All you need to do is to ride the elevator and get the Blue Orb Fragment found at the top. But you have to watch out, because this time, enemies are now in their DT form. To make things worse, when 6 Hell Prides are on the elevator with you, the elevator cannot sustain the weight and will fall. So you need to make sure you eliminate your current enemies before another wave comes down from the top.
SECRET MISSION 5: Mission 9, This one can be found inside the Limestone Cave in Mission 9. It is in front of the entrance (it's a small opening above). Jump on it and go through the path until you see red glowing crystals.
OBJECTIVE: In this mission, you have to destroy hidden objects within 40 seconds. There are 50 of them and that includes wine bottles, tables, chairs, menu board, barrels, glass and jukebox. You can farm this secret mission if you are low on Red Orbs.
SECRET MISSION 6: Mission 10, It is in Mission 10 where you can find it at the right of the statue where you have obtained the Neo-Generator. It is portrayed as a white tombstone-like structure.
OBJECTIVE: Collect all of the 50 Red Orbs within 30 seconds.
SECRET MISSION 7: Mission 11, This mission can be found at the beginning of Mission 11. Before you enter the first door, there is a ledge at the left; jump onto it. Double jump away from the wall, Air Hike, then perform Sky Star towards it. Now you will stand in an area where there is a red portal. Alternatively, you can get there with only Level 1 Trickster Style by wall running up the spiral pillar opposite the ledge, jumping off, then Air Hiking (if necessary) up to the red portal area. For Vergil, jump away then use Aerial Rave towards the wall and quickly perform Trick Up.
OBJECTIVE: Obtain the blue orb fragment within the time limit
SECRET MISSION 8: Mission 13, This one can be found at one of the lights glowing red in the Spiral Staircase in Mission 13.
OBJECTIVE: In this mission, you have to defeat all of the enemies with NO TIME LIMIT. There are 3 white Arachnes, 2 green Arachnes and 2 Hell Vanguards.
SECRET MISSION 9: Mission 13, This one can be found in a crystal puzzle in Vestibule in Mission 13. It's in the ledge at the left of the corridor, portrayed as a bull with red shining eyes.
OBJECTIVE: In this mission, you have to kill all of the enemies riding in a "wagon" before they escape.
SECRET MISSION 10: Mission 16, This one is in the white panel to the right where you find the Golden Sun in Mission 16.
OBJECTIVE: In this mission, you only have to solve the puzzle, so you only need your own intelligence. All you have to do is to pass the light to the other statue just in that area. You don't have to pass it to the small corridor to the upper right corner.
SECRET MISSION 11: Mission 17, This one can be found in one of the glowing panels above the ledges in the Pitch Black Void area in Mission 17. You will be transported to the Trial of Skills.
OBJECTIVE: In this mission, you have to reach the other end of the area where there is a Blue Orb Fragment. Use Trickster Style.
SECRET MISSION 12: Mission 18, This secret mission can be found during Mission 18 in the Netherworld. It is located at the left side of the leg statue and it is portrayed as a rectangular tablet.
OBJECTIVE: In this mission, you have to reach to the top in order to obtain the Blue Orb Fragment. The mission will fail if you will enter any kind of the door (this leads back to Netherworld). Now, in this mission, you are now in the God's Cube Chamber. You need the Air Hike and Sky Star. It's because you have to jump over the rotating and moving cubes in order to reach the top. Air Raid is optional, but it can be also needed when you are not good at timing