Many, if not all, of the following similarities between the two games are the intentional results of the S3 Plan. The aim of the plan according to Revolver Ocelot was to turn a rookie such as Raiden into a recreation of Solid Snake. However, it is later revealed by JD that this is not the true aim.
- The first boss is a short-range gunfight with obstacles blocking the player's line of vision and preventing him from getting close to his opponent: Revolver Ocelot in Metal Gear Solid, Olga Gurlukovich in Metal Gear Solid 2: Sons of Liberty. Explosives are the worst enemies to Snake in both of these battles. If Snake steps over the square line around Kenneth Baker or uses an explosive weapon to combat Ocelot, the entire room will be filled with explosions. Olga can toss grenades at Snake, which can cause him serious damage or death. Also, both bosses are of Russian descent.
- Each enemy leader pilots an aerial assault on the main character during a transition between two areas: Liquid Snake attacks Snake with a Hind D on the communications tower, and Solidus Snake attacks Raiden with a Harrier II on the Shell 1-2 Connecting Bridge. Although both aircraft are destroyed with stinger missiles, the area where the battle occurred is destroyed in the fight, and the pilot is quickly revealed to have survived.
- Both Vulcan Raven and Fatman play a game of cat-and-mouse with the main character while firing automatic weapons at him. The field of each battle is cluttered with metal storage units that the enemy occasionally targets with his main weapon: Raven destroys crates to impede Snake's movement, while Fatman plants bombs that will destroy the entire heliport if not disarmed.
- Raiden's battle with Vamp is similar to Snake's battle with the Cyborg Ninja: both bosses run and leap with great speed, both are capable of escaping from sight for a time, both are immune to gunfire under certain circumstances, and both close in for melee combat once they are sufficiently wounded.
- Metal Gear REX and Metal Gear RAY are both especially vulnerable in their open mouths, and both can only be destroyed by Stinger missiles.
- The final battle in each game is fought in close quarters in an open, flat, high-elevation area. Liquid and Solid Snake battle bare-fisted atop the wreck of Metal Gear REX. Solidus and Raiden battle with swords in the shadow of the wreck of Arsenal Gear. Both Liquid and Solidus will charge at their opponents, potentially causing heavy damage or knocking the main character off the battlefield to his death if he leaves himself open.
- The scene where Raiden sees the soldiers killed by Vamp is similar to the one where Snake sees the Cyborg Ninja for the first time. The similarity is underscored during the initial revelation of the S3 Plan, which transposes flashbacks to the two scenes.
- The appearance of a Cyborg Ninja in a role that alternately assists and antagonizes the main character. Both Cyborg Ninjas are bosses in the games in which they appear, although Olga is a boss before she becomes the Ninja.
- An identical exchange of dialog occurs between Snake and a mysterious stranger, telling him there are claymore mines in a location, he should use a mine detector, call the person "Deepthroat," and that the mysterious caller is "one of (his) fans."
- Both Cyborg Ninjas reveal themselves during the Metal Gear battle and sacrifice themselves to save the main character. Their reasons for doing so are related to their relationships.
- The beginning of both games involves a vessel called the Discovery.
- The codename of the operative being "Snake", although Jack's is changed to Raiden very early into his first mission.
- A character directly tied with a "president" is held hostage, although he isn't what he seemed to be at first, and his killed by a heart-related condition. In Metal Gear Solid this is DARPA Chief Donald Anderson, who had been heavily bribed in order to back the REX project. However, he apparently died of a heart attack, and it's later revealed that the "DARPA Chief" that Snake encountered was actually Decoy Octopus in disguise, the real Anderson was killed by Ocelot in a botched torture session, and FOXDIE was responsible for his death. In Metal Gear Solid 2 this is Secret Service Agent Richard Ames, who was held hostage by the Sons of Liberty, but in actuality, was a DIA agent planted in by the Patriots to keep tabs on Raiden, and was killed via his pacemaker's nanomachines shutting down to simulate FOXDIE. Similarly, both Anderson and Ames shared the same Japanese voice actor.
- A "president" is kidnapped in both situations. In Metal Gear Solid it was Kenneth Baker, President of ArmsTech. In Metal Gear Solid 2 it was the President of the United States, James Johnson.
- A "president" dies shortly after meeting the main character and Revolver Ocelot. In Metal Gear Solid, Kenneth Baker dies after coming into contact with Snake from the effects of FOXDIE. In Metal Gear Solid 2, James Johnson is shot by Ocelot after Raiden refuses to kill him. On a related note to the two above, both "presidents" were voiced by the same voice actor in the Japanese version.
- Vulcan Raven and Vamp respectively refer to Ocelot as "General Ivan" and "Crazy Ivan", a racial ephitet for someone of Russian ethnicity.
- Revolver Ocelot calls Snake a "carrier boy" in the torture room, his subtle way of talking about the FOXDIE that Naomi Hunter injected into Snake. He also calls Raiden that after he shoots President Johnson, referring to the disk that contains the virus to destroy GW that Raiden is holding.
- The leader of the terrorist group in each game is a clone of Big Boss: Liquid Snake in Metal Gear Solid, Solidus Snake in Metal Gear Solid 2. In both games, the character's use of the codename "Snake" is played up in contrast to Solid Snake early in the mission.
- Both of games take place in a far off, remote American facility that is secretly housing a new Metal Gear (Metal Gear REX in Metal Gear Solid, and Arsenal Gear in Metal Gear Solid 2).
- Revolver Ocelot is a member of both terrorist groups, and is effectively the second-in-command of each group.
- Otacon and Emma Emmerich fulfill similar roles in each game. In addition to the fact that they are stepsiblings, both are gifted scientists who worked on the latest Metal Gear in order to overcome issues with their family: Otacon to atone for his grandfather's actions, Emma to gain revenge against Otacon and to force him to see her as a woman. Both also wet their pants upon being revealed for the first time in both games.
- In addition to the previous, both Otacon and Emma hide in lockers and fear their rescuer.
- The player is given the option to save a female associate from death at the hands of the terrorists. Snake can choose to give in to Ocelot's torture and let Meryl Silverburgh die, although canonically, he endures the torture and she lives. Raiden saves Emma from being instantly killed by Vamp, although the wounds that Vamp inflicts on her ultimately prove to be fatal.
- The torture room in Metal Gear Solid 2 is an exact recreation of the same room in Metal Gear Solid. The cell that Snake escaped from in Metal Gear Solid is visible through the window in the torture room in Metal Gear Solid 2. In both games, the player may be freed by the Cyborg Ninja, although Snake can escape from his cell in Metal Gear Solid before being rescued by the Ninja.
- both events have a revelation where a character is not who he appears to be, and it is found by tracing the frequency origin of that character to within the enemy compound (Master Miller as being Liquid Snake in Metal Gear Solid, and Colonel Campbell as being an AI construct made in his likeness by GW in Metal Gear Solid 2).
- Main characters support team has member who doesn't complain about main characters cigarettes but tells him not smoke too much (Nastasha Romanenko in Metal Gear Solid and Solid Snake in Metal Gear Solid 2)