Once you're swimming around below DK Isle, get behind the waterfall (as shown in this screencap). Look at the ocean floor below on the right, and you'll see a large, blue trapezoidal void. Turn right and swim directly into it. Your Kong should disappear. When it does, adjust your camera with R and/or C-Up, and you'll appear inside the cockpit of K.Rool's escape ship!!
It's a room with five vidscreens. Two show static, two show radar blips, and the middle one is a map of DK Isles. (It reminds me of the map of Treasure Trove Cove that could be found in the Rusty Bucket Bay level of Banjo-Kazooie.) Even though the back of this room looks like a huge open door, you can't leave through there. Instead, leap behind the computers and fall through the blue void in the floor to escape. There's nothing much else you can do in here, but...
If your Kong is still swimming when you enter this room, it will look like he's floating in zero gravity because technically, there's no water in here.
It looks funniest with Lanky because his arms are so long.
Chunky in zero gravity.
This is the actual cutscene the room is used for (accessible on your Mystery Menu in DK Theatre under "K.Rool Press Button").
It's much darker in the cinema than it is when you enter it.
Now, I guess the question is why did Rare choose to store this room underneath DK Isle? This is only a theory of mine, so don't accept it as fact, but I think it has something to do with the fact that K. Rool's ship crashes near the area where you can get into this room. It is the cockpit of the ship, so maybe there's a connection? The room will always be there, even before the ship crashes, though. Maybe it was just placed here for convenience.
If you are having trouble accessing this room, you can download this video of me taking Chunky into it from underneath the island, behind the waterfall: