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

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.

Two members of the terrorist group Dead Cell were cut from the game. One of which was Chinaman who was based off of Jet Li. He was suppose 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.

Two members of the terrorist group Dead Cell were cut from the game. One of which 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.

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.

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

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 Kojima decided to change the story so Ocelot received a transplant from the deceased Liquid Snake, creating Liquid Ocelot.

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.

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.

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.

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.)

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.

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.

When the AI colonel starts going haywire, one of the things he will say is "Infiltrate the enemy fortress, Outer Heaven! Destroy the final weapon, Metal Gear!", a paraphrasing of the first radio message Snake receives in the original Metal Gear. Furthermore, while Raiden is receiving this message, the frequency monitor is replaced with the opening cinematic of the MSX2 version of Metal Gear.

According to the first volume of Metal Gear Saga, Liquid Snake, Spoiler:having faked his own death from the FOXDIE virus, was meant to be the main antagonist of the Tanker Chapter (an aircraft carrier during this part in development). However, this, along with most of the original plot, was scrapped due to tensions rising in the Middle East.

Hideo Kojima decided to have Harry Gregson-Williams compose most of the game's soundtrack after Kojima and sound director Kazuki Muraoka watched "The Replacement Killers" in a cinema, and enjoyed the music that Williams composed for the film. They had planned to watch "Saving Private Ryan", but the line for the movie was very long.

Gregson-Williams was given limited descriptions of the music he had to compose, such as "heroic" or "stealthy" as Kojima wanted the music to be pure Gregson-Williams. Gregson-Williams was told that the limited instructions he got was due to language barriers.

During one of the final scenes in the game with Spoiler:Snake and Raiden in New York City, Vamp can be seen standing behind them in the distance by adjusting the camera. This rewards the "Vamp Eyer" achievement/trophy on applicable platforms.

On the Tanker mission, the cooking pans found in the kitchen area each play a different note when shot, and are arranged as a musical scale so that the player could play music on them.

Bande Dessinée, a digital comic strip retelling the story of Metal Gear Solid 2: Sons of Liberty, has a number of significant differences to the original game's story:
• The Tanker Incident is portrayed through flashbacks at several points throughout the story instead of being shown in full at the beginning.
• Spoiler: Peter Stillman never fakes being unable to walk and never mentions the church bombing that haunted him in the game. He accompanies Raiden to the battle Fatman, and a video of Fatman appears when Stillman activates the last C4 who calls out Stillman by name and gloats about how he had the last laugh.
• Spoiler: The Sorrow appears in one of the new scenes which the spirit of Liquid Snake enters Revolver Ocelot's mind and talks with him about how he is able to possess him scenes.
• Spoiler: A flashback never seen in the original game of Raiden's childhood as a child soldier was added during Raiden's torture under Solidus Snake.
• Spoiler: Snake is the one to fight Vamp in the purification chamber and escort Emma Emmerich to the computer room.
• Spoiler: During the fight atop Federal Hall, Solidus knocks Raiden out. Snake then appears, having failed to follow Liquid Ocelot in the stolen Metal Gear RAY, and challenges Solidus to a sword duel.

In the Substance version of Metal Gear Solid 2, completing all of the VR and Alternative Missions with Raiden unlocks a version of Raiden in Gray Fox's ninja exoskeleton to play VR and Alternative Missions with. His only pre-equipped weapon is the H.F. Blade. This could imply that before Spoiler:Olga died, she gave Raiden her suit to use alongside the blade so he could train as a Ninja.