After defeating Solidus Snake at the end of the game, he falls to his death from the Federal Hall building. Just before he falls however, if you look closely, you can see his lips move slightly in the brief moments that they are not covered by the collar of his exoskeleton. By replacing Solidus' model with Solid Snake's (who shares most of his facial features) through mods, it reveals that Solidus was actually saying one last message to Raiden. However, the dialogue during this moment is still muted, so his last words remain unknown.

Solidus Snake's swords are named "Minshuto" and "Kyowato". This translates to "Democrat" and "Republican", respectively.

In order to hide the twist of Spoiler:Snake being a decoy protagonist and Raiden being the true main character, director Hideo Kojima personally put together the game's trailers himself. The footage for the E3 2000 trailer was recorded from Spoiler:the Tanker segment at the start of the game, when Snake is the playable character, and in the E3 2001 trailer, Spoiler:several scenes that focus on Raiden in the actual game were edited to swap him out with Snake.

According to Hideo Kojima & Yoji Shinkawa in the documentary on the making of Metal Gear Solid 2 from the game's bonus disc, Shinkawa stated that Rosemary represents Kojima's ideal, classy and intellectual woman. Some of Raiden & Rosemary's conversation were influenced by Kojima's own life experience.
Kojima stated that the idea for April 30th stemmed from his relationship with his wife, where she kept reminding him about that date before they were married. One evening, he had a date with his wife, but he completely forgotten about it, which caused him a lot of crisis in their relationship.

In a 2004 interview with GameCenter CX, Hideo Kojima revealed a pair of jokes that were dropped from the final game:

Solid Snake can grow his facial hair after being shaved. If the player picks up the Shaver in Strut A of the Big Shell near the Deep Sea Dock, and give it to Snake when they first meet on Strut B, he will be clean shaven when they see each other again after escaping the Torture Room. However, if the player waits a week his facial hair will grow back.

During the Plant chapter, several Mo'ai statues can be found in different locations on the Big Shell:
• Strut D: Among the scaffolding above the pool.
• Shell 1 Core, B2 Computer Room: Underneath the south-western computer desk.
• Strut L: In the far corner of the small room behind the windows.
• Shell 2 Core, 1F Air Purification Room: In the vents, using the Nikita.
• Shell 2 Core, B1 Filtration Chamber No. 1: Underneath the wreckage, underwater.
• Shell 2 Core, Locker Room (Where Emma Emmerich is hiding): It's hiding inside the locker (This locker can only be opened in Extreme mode. However, there's a Claymore mine that is set inside the locker, which will kill the player instantly if it's not destroyed or picked up).
• Strut E: In the room with the Digital Camera, behind the northernmost boxes.

During the Tanker mission, if Snake saves his game, Otacon will try to recite proverbs like Mei Ling in Metal Gear Solid, except he will always mess them up. If you save your game and listen to Otacon's increasingly disjointed advice 13 times, a final codec call will be shown where in the middle of Otacon reciting a proverb, Mei Ling will enter the call via an audio-only transmission and interrupt him. She tries to correct him with a misplaced "cheat sheet" she made for him, and then scolds him for losing the sheet and butchering proverbs with his own interpretations. Mei Ling will then tell Snake the correct meaning of the proverb, tell Otacon they have unfinished business, and leave the call. This is Mei Ling's only appearance in the game.

According to Hideo Kojima in the documentary Metal Gear Saga Vol. 1, the game's original setting would have revolved around nuclear weapon inspections in Iraq and Iran. The plot of the game involved Solid Snake stopping the new Metal Gear while it was located on an aircraft carrier within a certain time limit. "Liquid Snake" and his group were supposed to be defeated by Snake, which would imply that Liquid would have faked his death from FOXDIE in "Metal Gear Solid (1998)". However, after working on the project for 6 months, tensions began to rise in the Middle East, so the team decided to scrap it in order to avoid controvesy. The final result of this original plot we relegated to the game's opening, involving "The Tanker".

In the hostage room on the B1 floor of the Core in Cell 1, hitting the hostages enough times triggers an angry call from the Colonel and Rose. This also causes the player to be unable to save the game by calling Rose.

In the original design document, it was possible for the Spoiler:hostages to die after Metal Gear Arsenal was activated. Around 50-60 bodies would have been able to be seen in the water, with the water being red from their blood, which in turn attracted sharks into the area. Both Snake and Raiden would have to go through the area afterwards.

Raiden (雷電) in english means "thunder and lighting" or "thunder god." The character shares this codename with the Mitsubishi J2M Raiden, also known by the allied forces as "Jack," this was an Imperial Japanese fighter aircraft used in World War 2. The patriots had named Raiden after the plane and later let him know that, just like his name, he was simply a weapon, a tool to be disposed of once it completed its purpose.

During the Tanker Mission, if the player looks at one of the girl posters in first person view and calls Otacon, a conversation will start where Snake appears to stare at the poster in awe while Otacon tries to convince Snake to remember the mission.

The HD Collection rerelease will award the player with the "Snake Beater" trophy/achievement upon triggering this.

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.

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.

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.

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.

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.

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.

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.