The beginning of the mission involves using a cargo-plane to perform a High Altitude Jump into an enemy region, and then working the way to the destination.
The initial mission of rescuing a scientist from enemy territory becomes more complicated as to revise the entire mission.
The female contact ends up getting romantically involved.
The female contact also gives explanations over the radio about the various locations of the enemy region.
The main character ends up fighting their former mentor(s) and at least one of them giving a speech on how the loser of the fight is liberated from the battlefield and the winner will have to remain to fight a lifetime of endless battle. Similarly, their former mentor(s) also tells the main character to "go home" at one point at a bridge.
The ending ends up having the main character going into Alaska with their love interest, only for one of them to abandon the other.
Because of the main protagonists actions, it was implied that the enemy territory they infiltrated also ended up ruined as a result of their mission (in the ending, Ocelot reveals that Graniny Gorki as well as Groznyj Grad, one of the OKB labs and the main military base of the Soviet region of Tselinoyarsk, respectively, were destroyed by a Davy Crockett, and Zanzibar Land ended up collapsing due to the "death" of Big Boss).
The main character, before going to a fight to the death with its former mentor, has to pass by an ally of its mentor controlling a great tank capable of launching nuclear warheads (in Metal Gear 2, Snake has to destroy Metal Gear D as well defeating Gray Fox, the pilot, and in Metal Gear Solid 3, Snake has to destroy the Shagohod as well defeating Volgin).
A boss battle spans a larger battlefield than normal and the boss isn't found under normal circumstances.
One of the pen-ultimate boss battles involved a fistfight in a treacherous and small area (Gray Fox and Solid Snake fought in a small room surrounded by mines; and Colonel Volgin and Naked Snake had a fistfight in a makeshift "ring" created by lowering an elevator).