This page contains information regarding new Star Trek material, and thus may contain spoilers.
Nibiru was an M-class planet, and the homeworld of the Nibirans, a primitive pre-warp species. While the planet resembled tropical regions of Earth, it possessed red instead of green flora. It was also the home of an unknown species of docile quadruped mammals and large fish.
To avoid breaking the Prime Directive, a disguised captain Kirk entered the Nibiran settlement and stole their sacred scroll, drawing them into a chase. McCoy appeared with the quadruped, but Kirk accidentally stunned it, forcing both of them to run and dive into the sea. Meanwhile, Sulu and Uhura rappelled Spock in an environmental suit down into the volcano, to stop the eruption with a cold fusion device.
From the bridge, Kirk, McCoy, Uhura, and Sulu learned they would not be able to beam Spock up due to interference from the volcano. Despite Spock's demands to leave him while the device detonated so as to avoid breaking the Prime Directive, Kirk opted to lift the Enterprise out of the sea and fly to the volcano to get in range. Spock found himself in the transporter room greeted by Kirk and McCoy, but could only think about the Prime Directive being broken.
Although the Nibirans saw the Enterprise, Kirk covered up the incident in his captain's log, prompting Spock to write an accurate report. Admiral Pike admonished Kirk on his return to Earth, and informed him the Admiralty were returning the Enterprise to him. (Star Trek Into Darkness)
Production designer Scott Chambliss noted everyone on the crew wanted to start Star Trek Into Darkness on a tropical planet, but wanted it to feel special and different from Earth. "So I thought, 'Well, we don't want it to be green.' I constantly go to Hawaii, and one of the things I love there is lipstick bamboo. Portions of the trunks are this beautiful magenta. I took a photograph of timber bamboo, a beautiful jungle of it, and played with it in Photoshop and turned it really deep ruby red, and it was beautiful." 
J. J. Abrams scouted Hawaii as a shooting location, but opted not to film the sequence there.  An outdoor set was constructed in Marina del Rey in California. According to Dan Mindel, "We shot [the scene] all at night so we could control the lights and manipulate it so that the steam that we were making would block out the sun and give us a lot of texture. All the sparks and fire is real." 
When quizzed for an in-universe reason the Enterprise was hidden underwater, Roberto Orci said a "line of sight [was] necessary given [the] unstable and shifting magnetic field of [the] super volcano on alien planet. That's why no beaming. Gotta physically get back to the ship." Alex Kurtzman came up with the image of the ship rising out of the sea, but they acknowledged fans would find it questionable so they wrote Scotty's line questioning Kirk's decision.