The level begins off in a large hallway that you'll be going back and forth few times. There are few corridors filled with Assault Troopers and Assault Enforcers, and a couple of Sentry Drones. You must go to the middle of the upper path and press the 3 buttons on each side of the main pillar to open the area right at the opposite direction of the button sets.
Behind each opened wall is an area filled with Slimers, eggs, Octabrains, Assault Enforcers and plenty of water! Both of the rooms follow the same layout. You must go to the middle room, kill enemies inside, then dive into the small alcove pool and press the button, which will reveal a lever immediately to the right which must be pulled. A room with machinery will then open up in the larger water area. You cannot go there from the hole in the middle room because it has an invisible forcefield, so swim up and go dive down from the water around the middle section. You should quickly find the opened area where there is some machinery. Use some simple aiming and quick swimming to get past them, and be wary as the machines are slightly different in the two rooms. Once you retrieve the keycard from the end of the machinery, you can head back to the middle room and see a door is open. Oops! There was a Mini Battlelord hiding in there (Yes, there is one in both areas). The fight can be a little tricky since there is very little cover and the Mini Battlelord can quickly roast you if you don't dispose of it with careful usage of Devastator, RPG or Shrinker. Once its dead, collect the health and ammo from the room you opened and use the keycard. This will open up a part of the blockades on the other side of the Purple Radioactive waste.
Once both areas have been cleared, you have found the Yellow Keycard behind the Mini Battlelord at the other section, you can go and open the door. Luckily you WILL find Protective Boots in this level, and there is no way to deplete them before you reach the Purple Radioactive waste, as it is the only hazardous floor type on this map. MAKE SURE TO ACTIVATE RUN MODE! You will need to quickly make yourself across the purple waste, straightest way, to the other side and open the door. Most likely your boots will get depleted by the time the door opens, so you will suffer few drops of HP. Use any portable medkit you find here.
You emerge into a room with ammo and Scuba Gear. Swim down the water and you will find 2 Atomic Healths in the first water area to increase your life to maximum of 200! Keep swimming and you find the way to the big chamber, where the Alien Queen is. Boss fight emerges!
Fighting against the Queen is, with enough ammo, pretty simple. All you should do is keep swimming around and nuking her with all your RPG and Devastator ammo. She will constantly spawn more Drones, but they move rather clumsily underwater so ignore them and just focus on the Queen. It will take some time longer to deal than the Overlord or the Cycloid Emperor, but it should not prove too difficult. Once defeated, cinematic pops where Duke sticks a Pipebomb into the Queen's "private section" and swims to the surface / away, while the Queen's corpse explodes into a pile of blood and gore.
Congratulations! You have completed Duke Nukem 3D Atomic Edition!
There are 7 secrets in this level. However, due to symmetrical design of the level (cause by availability of the Duke-Tag game mode), most of them can be grouped together.
Secrets #1-4: Balconies
They are located in the corridors on the sides of the purple lava. There are 2 on the green side and 2 on the brown side - situated on the sides of the door where you enter the are with water. You need a jet pack to reach the balconies - one can be found underwater on the brown side, inside a small aquarium-like room with 2 switches.
When you have the jetpack, simply fly onto each of the balconies to trigger the secrets. The ones on the brown side contain 2 packs of rockets for devastator and 2 boxes of ammo for shotgun and the ones on the green side contain 2 boxes of ammo for chaingun cannon and 2 boxes of rockets for RPG.
Secrets #5-6: Alien pipes
These are also located symmetrically on green and brown sides. They are behind the main gate leading to those 2 areas, but outside of the main structures. You can access them from behind - on the green side, opposite to the place with air tank and on the brown side opposite to the place with protective boots. They are accessed via the organic-looking, alien holes on the walls.
Each of the secrets contains ammo for RPG, chaingun cannon, devastator and shotgun, box of pipebombs. The one on the green side also contains 2 small medkits. Aside from being secrets, they can be useful for fighting the mini battlelords inside the structures, as the other end of the pipes leads inside the structure from a good sniping point.
Secret #7: Gasping for air
This secret can be reached during the boss fight with the Queen. You might have noticed there are a couple of holes in the ceiling of the underwater cave the fight takes place in - 3 of them to be exact.
The secret is located in the hole directly in front of the entrance to the cave. Just swim there and emerge from water when you reach the hole, then climb onto small rock shelf with atomic health, portable medkit and an armor, which all may prove crucial during the fight. Also, all of those holes may be useful for avoiding the Queen's electricity attacks.
Achievements (Megaton Edition Only) Edit
Damn I'm Good: Complete this level on any difficulty to earn this achievement.