You start with the cutscene explaining about the underworld of Atlantis. After that you get to create your own superhero team. It's optional but you're better off sticking with your default team which is Captain America, Thor, Spiderman and Wolverine.
The first part shows your team putting nanotechnology in their body so they can breathe and move around the water without the need to go up to get some oxygen before you dive down again. Instead, you can move around the water like you do in the air with the exception that jumping is replaced by swimming up and to go down is to move so it automatically goes down to the seafloor.
Swimming into Battle
After you go to the connection tube to the diving chamber, once you go in, you're teams journey starts. The Atlanteans believes your team is a threat so you're going to battle their army throughout this level. It's quite easy to get through because you're ability to swim up and down in heights and not worry about getting hurt but you should at least be wary of mines which would be the only threat. Once you reach where Namor is trapped, you have to take care of the remaining enemies before going to the console and freeing him from the bubble.
Namorita came from the seeline and is able to rendor Namor unconscious since he's in no shape to fight. As an option, you can go through Temple of Negrete to get Walek Seaweed by finding two Eye of Negretes and a Trident's Tip to open the place at the end for that source.
Atlantean Trenches shouldn't be hard to go through. Byrrah and Krang will be the first two water villains to deal with. As long as you have a full team, you'll be able to defeat them easily. Then find the three sonic emitters and destroy them to succeed. Then make your way to the Atlantean throne.
The Key to the Throne
The Atlantean throne has one puzzle which you need to overcome. Despite taking out all the enemies, you need to take one bead at the beginning after you save from the SHIELD icon that you see on your map. Bring it to the middle to open to sides which is left and right with the vortex at opposite sides of the room. If you're brave enough, you just need to keep tapping the jump button to swim up to get to the other sides to get the remaining beads and put it on the center where the other bead is.
Attuma and Tiger Shark
Attuma and Tiger Shark can be tough to deal with while they were swimming in the air. You should use to console on either ends to be able to get the better of them when their grounded. The console will suck the Attuma and Tiger to the ground to make it easier for you to fight them in. Repeat this pattern alternately in opposite sides as the water will be sucked in a limited time before you have to reach the console again. After the fight, Tiger reveals the intention of Dr Doom before they disappear.another strategy would be to change to all ranged attack characters at the S.H.I.E.L.D save spot and use that to your advantage.
Kraken the Water Lizard
Go through Defender's Crypt taking out the remainders of the Atlantean soldiers. When you enter the Arena, what we supposedly believe is Mandarin underwater but in reality he does not. Anyway the surprise is the Kraken which is a large green water lizard. He can't be hurt by normal means. Defeat Kraken using this pattern. After you take down his guards, once the column is open, go in and it will start the button minigame or Wii motion minigame. Do this to all four columns and the giant creature would be defeated.
When you are finished, Namor will congratulate you and allows you to leave this area.