There are 5 secrets in this level.
Secret #1: Diving in
This secret can be visited before going aboard the ship. To find it, dive underwater and swim under the boat. You should notice a little hole in its hull, marked with yellow and black stripes. Swim to it and emerge from underwater there. You will have to face 1-2 alien beasts. Then simply walk in the small corridor and collect night vision googles, armor, chaingun cannon and steroids.
Secret #2: Playing in the kitchen
Inside the dining room/kitchen of the ship, walk towards the small part with ooze cans. There you should notice some cupboards covered in blood and bodyparts. On one of those cupboards, with a head and a knife on it, there is a switch. Flip it and a small room with a portable medkit will open on your left.
Secret #3: Duke is on TV
Inside the barracks on the ship, there is a room with some assault troopers as well as a couch and burning TV. Simply jump on the TV and that is where the secret is located. Behind the TV there is chaingun cannon. Aside from that, a small place will open in the opposing corner of the room where a shotgun is located.
Secret #4: Nasty captain
This secret is located in the captain's room, where the red keycard is located. Just above the desktop where the keycard is, there is a clock. Press use/open in front of it and the bookcase behind you will go down as well as the wall behind the bookcase will open. There is a secret room with shrinker, 2 ammos for expander, 2 atomic healths and some of the captain's nastier toys.
Secret #5: Boxes and cranes
Behind the yellow keycard forcefield, locate the room with 1-2 assault commanders and a giant stack of boxes. There should also be a crane operating them as well as conveyor belt. After dealing with the enemies, climb up the boxes. Another assault commander should emerge from between them - kill him and jump to the space behind boxes where he was waiting for you. Now turn towards the wooden boxes without metal frames on them - there seems to be one box missing under a bigger one. Walk in that place and collect the RPG and protective boots.
The name of the ship on this level is Valdeez-2, and the captain's room contains liquor bottles and a bed. These are all references to the real-life Exxon Valdez oil tanker, which ran aground in 1989 because its captain had fallen asleep due to excess drinking.
Although published later as part of the Plutonium PAK, Derelict was one of the earliest levels designed for Duke Nukem 3D. The final version is almost completely unchanged from E3L2 of the December 1994 prototype.