Level portal location (hub access): Cloud Cuckoo Land (lower area) - Next to the submarine in the watery lower area
Everyone else will sprint away when the level starts, leaving Vitruvius and Benny the arduous task of catching up to them. Take control of Benny and shoot the floodlight overhead to get the parts to plug the leak in the sub. Head to the far left and smash the crate to find a record for the sound system. Take it back and pop it in place for the floor to collapse underneath you (completely by itself, not the sound, no).
Minikit 01/05 - Heat Ray (Bad Cop)
After the sound system smashes a hole in the floor and you drop down, to the left will be a golden wall of rubble. Melt it down to find the first minikit.
Minikit 02/05 - None
After using the master build spot for a lift, the minikit should be above you (when you are standing on it at the top of its path) behind a grille.
Once the bodies hit the floor again, head right into the cave-like area and break the rock on the back wall. This creates either a cloud or a leak (I couldn't be sure which) and puts out the nearby fire. Smash apart the damp fire to find a secret knock spot for Vitruvius. Once the wall opens up, head to the new area on the wall and smash the pipes on the right wall. This gives you the final part for the master build spot. Create the large swinging platform and jump up it to the higher area.
The giant apple being supported by clouds on the back wall can be destroyed, dropping both Benny and Vitruvius to the depths of the sub. In the middle of this new area you should be able to see an inaccessible terminal for Benny to hack. To open it up, smash the speakers on both sides of the area, turn them into pressure panels and activate them. This will open up switches on the left and right of the terminal. Once both are flipped, Benny can finally start hacking.
Succeed in the infiltration and a torpedo will make your life interesting. The sub will fill with water and both of you will have to exit the sub from the roof and circle around to the left to find the crashed torpedo. Shoot the wreckage to blow open a small cave and swim inside.
The path in the cave is quite linear (unless you are collectible gathering with the collectible section below), so follow the tunnel along. Shoot any divers in your path until you reach the giant swordfish area.
Minikit 03/05 - Destroy 5 treasure chests, Projectile (Benny) or Heat ray (Superman)
The first chest is just past the first air point and the save point. The second is just after the next air point. The third can be found just after the golden wall of rubble. The fourth is just before the large open swordfish area. The final chest is at the bottom of the giant swordfish area. Break it open for the third minikit.
Pants - Destroy 3 golden puffer fish, Heat ray (Superman)
After the second air point in this area you will spot a golden rubble wall on the left. Burn it down to find a new area. In this small area will be three golden puffer fish to melt down, The first will be directly in your path as you travel left. The second will be in the center of the large open area. The third will be in a hidden cave in the rock at the top right of the large open area. Once all three are gone, they will drop their pants (...wait, what?). To get back to the previous area, take the top path out of the large open area.
Minikit 04/05 - None
Before reaching the giant swordfish area, look along the roof of the tunnel for the fourth minikit (it is directly above the third treasure chest when looking for the previous minikit). Swim into the hidden tunnel (on the left side of the minikit) and grab it. If you need air, stop at any of the bubbling points in the water and blue hearts will rise up to refill it.
Despite its intimidating looks, the swordfish is pretty easy to avoid. To progress you need to move over to the far right side (down the bottom) and find a yellow statue with a target on it. Lure the swordfish over until it prepares to charge and swim out of the way at the last second. It will ram the statue out of the way and destroy itself in the process. Head down the newly opened path until the area changes.
The new area is quite dark, but still very linear. The main dangers here are the moray eels (the pale ones and the giant electric one later).
Minikit 05/05 - None
Keep to the bottom of the tunnel as you travel along and you will find a spot that you can see water underneath (as in, only separated by a pretty thin line of rock). You can actually swim through this to reach the final minikit below.
Just keep swimming along, following the stud trails and breathing spots until you eventually meet the giant moray eel. You need to time your movements between his appearances. After you reach the top area again, hop out of the water and use Vitruvius's secret knock ability to open the door to reunite the group. Once you do, the level will end (Wow, what a linear level).
The Special - 150,000 studs
Obtain the above amount of studs to complete The Special and receive a gold brick.