In the computer room of the Shell 1 Core you encounter a parrot behind the same protective shield as Fortune. The parrot says things such as "HAL" and "Venus is Cancer". If the player uses the directional mic on the bird and says "You must be Ames" by pressing triangle enough times, the bird will repeat the phrase itself. Furthermore if you put the guards on alert enough times in that room the bird will begin to say some of their alert phrases as well.

The alternate name of the Patriots, the La-Li-Lu-Le-Lo, was chosen because the English 'L' sound does not exist in the Japanese phonetic alphabet, making it impossible to say. However, since there is no such sound that cannot be pronounced in the English phonetic alphabet, the concept could not be translated over.

Raiden's real name is Jack, and his girlfriend's name is Rosemary, or "Rose" for short. This is a reference to Jack Dawson and Rose Calvert, the main characters and lovers of James Cameron's 1997 hit movie "Titanic"

Both Titanic and MGS2's plots involve the sinking of a large boat (Though "Titanic"'s plot was based off of the real life tragedy.)

When Raiden meets up with Snake after he escapes and retrieves his stuff, he'll say "Time to go. If you run out of ammo, you can have mine." Then Raiden replies "You got enough?" Snake will say "Absolutely... Infinite ammo." while saying this, he points to his headband with his thumb. This is a reference to the original Metal Gear Solid where, if you get the good ending, Meryl will give Snake a headband that grants him infinite ammo.

Metal Gear Solid 2 pays homage to the film Titanic, in both characters and events. The game starts out on a tanker that sinks, followed by a sequence focusing on Jack and Rose.

During the Tanker mission, calling Otacon while staring at a bikini girl poster on the inside of a locker will cause Otacon to reprimand Snake, who will be pulling a face of awe. Hiding inside the locker and pushing Snake forward, Snake will kiss the poster. Leaning against the poster when the door is open and knocking on the wall will either cause a "boing!" sound if knocking on the girl's breasts, or cause the enemies to go into alert if knocking on her crotch.

Revolver Ocelot was going to Spoiler:have a mechanical hand after Ninja chopped it off in the last game. However, Liquid Snake was very popular with the fans, so Hideo Kojima decided to change the story so Ocelot received a transplant from the deceased Liquid Snake, creating Liquid Ocelot.

Hideo Kojima named the tanker Solid Snake sneaks onto the USS Discovery after the Discovery One from the movie 2001: A Space Odyssey.

While under cover, Solid Snake assumes the name Iroquois Pliskin. "Iroquois" means "Black Snake" in the Iroquoian language, Huron. And "Pliskin" is a reference to the character Snake Plissken from the film "Escape from New York", which was the main inspiration for the development of Solid Snake. Naked Snake (Big Boss), Solid Snake, and Solidus Snake each wear an eye-patch like Snake Plissken.

Two members of the terrorist group Dead Cell were cut from the game. The first of which was Chinaman who was based off of Jet Li. He was supposed to be fought in the filtration system where Raiden fights Vamp in the final version. He had the ability to walk on water, walls, and ceilings. He could hold his breath underwater for a very long time and had a dragon tattoo would come to life whenever he touched the water. However, he was cut from the end version and his abilities were given to Vamp. Chinaman is mentioned in the game as one of the Dead Cell members who died before the Big Shell incident.

The second cut member was Old Boy, a soldier who served in World War II and was a mentor to mercenaries and soldiers, including Big Boss. He was cut very early in development. However, he would have commanded troops in his fight against Raiden, and would have used guns and equipment from the WWII era.

When Snake is on the Tanker, Otacon tells him that Panzetamin prevents seasickness. After Snake tries it, Otacon explains that he experienced nothing more than a placebo effect and mocks him. As Raiden, if you ask about Panzetamin to Snake, he warns Raiden that it doesn't prevent seasickness.

The game had a scene removed where Snake is chased through the sinking tanker by a rush of water. Hideo Kojima said that it looked good, but wasn't fun.