When the player is spotted by an enemy, the game doesn't automatically enter the Alert Phase. The enemy has to call for back-up before the Alert Phase is triggered.
There is no longer a timer during the Alert Phase. Instead, it simply disappears when the enemy loses sight of Solid Snake.
Lockers have been included, as seen in Metal Gear Solid 2. Snake can hide in them, or hide bodies in them. This also applies to bathroom doors.
Like Metal Gear Solid 2, dog tags can be collected from enemies. Unlike Metal Gear Solid 2, however, there is no reward for doing so.
Boss Survival mode was added to the Special mode.
In the original, the cutscenes do not reflect Snake wearing the body armor if he has it equipped. This was changed in the remake for the most part, although there are still a few cutscenes that won't reflect it.
Like Metal Gear Solid 2, the pause screen has a map of the base, the original version just had the name of the area Snake was in.
Even if Snake finds a suppressor for the SOCOM in the remake, it will not be present in cutscenes. This is unlike the original, which has the suppressor visible in some scenes.
The Very Easy difficulty setting was added.
No VR Missions were included. In an interview, Dennis Dyack commented that VR training was to be included, but time ran out before the feature could be implemented.
In the PlayStation version of Metal Gear Solid, the player's life and maximum ammunition are gradually increased as the game progresses. In The Twin Snakes, both are at maximum from the beginning (as in Metal Gear Solid 2). In addition, the life bar is refilled after every boss battle, whereas in the PlayStation version it was only refilled partially after boss battles, and only completely after certain events.
Codec call skipping was added in, again mirroring Metal Gear Solid 2. Originally, pressing a button during a Codec call would result in the voice over stopping and the screens progressing manually. In the remake, there are two choices for call skipping. Pressing the B button mirrors the original game's manual progression, while pressing the A button will fast forward the call straight to the end.
Many environmental elements from Metal Gear Solid 2 were introduced into the remake, such as lockers, fire extinguishers, and others. In addition, many objects in the background can now be destroyed or broken, such as mirrors.
The M9 and PSG1T were added, as well as boss stamina bars, allowing for stamina kills on some bosses.
The books for distracting guards were introduced, featuring a picture of Alex Roivas, the main character of Eternal Darkness: Sanity's Requiem rather than a real life cover model. Similarly, the cover featured Ellia, one of the playable characters from the same game.
Sniper rifle controls were changed, making it possible to shoot while standing or kneeling. In the original, Snake automatically went into a prone position when the PSG1 was equipped while the scope automatically zoomed in.
Some cosmetic changes were made in the remake which are now incorrect when compared to later games. For example, Snake has light green eyes in the remake, where they are teal in Metal Gear Solid 2 and blue in Metal Gear Solid 4: Guns of the Patriots. Meryl Silverburgh also is now a brunette in the remake, despite having red hair in both the original and Metal Gear Solid 4.
The effects of snow were added in, a first for the series. While outside, snow will fall on the camera, fogging it up or frosting it slightly. Snow will also stick to Snake when he stands still and will come off all at once when he moves.
The thermal goggles were updated to show a more realistic representation of heat, as introduced in Metal Gear Solid 2: Substance. In the original, the thermal goggles tinted the screen red and significant objects such as enemies were a solid red, which was also shown in the first release of Metal Gear Solid 2.
Claymores placed by the player are visible. In the original, they disappeared after placement.
The Nikita missiles must be controlled in First Person View. In the original, the player could guide them in either First or Third Person View.
The AP Sensor was added for players who might play without the radar.
The PAL key icon changes color according to what temperature it is, rather than the player having to check its information screen as in the original game.
The radar mode "Caution" was added. Heavily armed attack squads also patrol the vicinity, as in Metal Gear Solid 2.
A "Game Over if Spotted" option was added for the Hard and Extreme difficulties.
The radar is replaced by an enemy's field of vision window if they spot footprints or something equally suspicious, as in Metal Gear Solid 2.
Bodies do not disappear unless they are discovered or after a certain amount of time has passed.
As with Metal Gear Solid 2, The Twin Snakes had a web site where players could submit Clear Codes that are displayed upon the completion of the game, and compare the results with other players. The website was open between March 9, 2004, and March 31, 2005, with a total of 20,405 codes submitted.
The player can now "hold their breath" in areas where they can't breathe. The player can do this by repeatedly pressing the Y button. This was first introduced in Metal Gear Solid 2.
The Briefing Files segment was updated from 2D animations of Snake to a fully 3D demo with Snake and now-visible Roy Campbell and Naomi Hunter. Both Campbell and Naomi are slightly fleshed out more as they can both be seen interacting with Snake. Also, Snake was naked in the original but wears boxers in this version.
Lights can now be shot and destroyed. For example, the heliport spotlights can be shot out.
PAN Cards no longer have to be selected to get through a security door.
The real time cutscenes activated during gameplay (i.e., looking through vents), have been replaced with pre-rendered FMV cutscenes.
At some points, the camera will go to a side-on view of Snake which it didn't do in the original (i.e. the Underground Passage, REX's hangar catwalks, and the hallway outside the prison cells).
Wires are now strung in certain areas for hanging (the wires were introduced in Metal Gear Solid 2). A noticeable example is in the Blast Furnace, where Snake has to crawl upon an outcrop from the wall. The player can choose to take the outcrop, or hang from the wire.
When Snake is pressed against a wall, he can move while crouched, whereas originally he would be unable to move (this feature was also introduced in Metal Gear Solid 2). This was criticized for making the Blast Furnace section easier. Originally, Snake had to crouch against the outcrop and remain there until the crane overhead would stop, and move again. The player had to time this section perfectly to avoid getting knocked into the molten metal below.
The ALERT, EVASION, and the CAUTION symbol that appears in the upper-right corner during these phases have been redesigned to look identical to how they looked in Metal Gear Solid 2.
The Stinger's lock on system was changed to look identical to Metal Gear Solid 2.
Guards now patrol areas they didn't patrol originally (i.e. the Canyon, and the section before REX's storage hangar).
The design of the elevator controls was changed to look like how they did in Metal Gear Solid 2.
Gun cameras have been put in some areas where normal cameras were originally.
Some glass windows can now be destroyed.
The styling of the Codec's HUD is made to look identical to that featured in Metal Gear Solid 2, but the character images were kept the same from the original version.
The zoom feature has been implemented into the cutscenes. The player can press the right trigger to zoom in on the cutscenes, and move around using the C Stick.
Trap doors in the floor will collapse in and fall down, where in the original, they were on hinges, and sprung back up.
Snake's punch-punch-kick combo is changed to the combo he and Raiden used in Metal Gear Solid 2.
Snake's walking animation has changed to look more smooth and realistic.
Snake's health can now go red, and slowly decrease as Snake bleeds. Snake can cure this by kneeling down to let the blood clot, or using the bandage item. All of this was first seen in Metal Gear Solid 2.
Due to the improved graphics, the GUI is now clearly visible on the many computers found around the game. One computer even has a Silicon Knights website on it.
Some items (i.e., cardboard boxes, suppressors, night vision goggles) have been moved to completely different locations than in the original.
Pipes can now be shot at, creating a cloud of steam that temporarily blinds enemies, and can cause enemies to be distracted.
The location and actions (physically) of the characters are completely different in cutscenes than in the original.
The player can now peek out over corners when pressed up against a wall, as seen in Metal Gear Solid 2.
Certain names and grammar have been slightly changed, i.e. the FA-MAS is now spelled FAMAS and FOX-HOUND is now FOXHOUND.
Some of the characters (e.g., Liquid Snake) were also slightly redesigned so that they'd more closely resemble their official artwork (in Liquid's case, the addition of dog tags during his appearances in both gameplay and cutscenes).
Some of the Codec calls were either omitted, extended, or changed in The Twin Snakes. For those that were omitted, some of it was due to either the gameplay elements associated with the calls (e.g., looking in the stalls of ladies bathroom to locate Meryl) being turned into default cutscenes, or, in one case, because of the removal of said gameplay element (e.g., the call about VR training, owing to the VR training mode not being implemented in the game in time before the release). Owing to this, one of Mei Ling's calls, specifically the call where Snake and Mei Ling enter a philosophical debate regarding whether it would be possible to save people's memories, was omitted.
Although the soundtrack was largely the same, the various bosses had their own boss themes in this game. Originally, the "Encounter" theme was used for the boss theme in general. Coincidentally, this also led to the Hind D and Metal Gear REX to share the same boss theme like in Metal Gear 2: Solid Snake. It is also to be noted that this technically made it the first Metal Gear game to have individual boss themes, predating Metal Gear Solid 3: Snake Eater.
In the original, the player had to return to the first building to find the PSG1 in order to defeat Sniper Wolf. In The Twin Snakes, it is located in the same position, though the PSG1T is available much closer, in the nuke building.
The disk change location is now at the bottom of Communications Tower A. The PlayStation version's disk swap occurred before entering the Blast Furnace.
The part of the gameplay when Snake has to look in the different bathroom stalls looking for Meryl is now an entire cutscene.
Because the remake starts the player off with a full life bar, the torture sequence is much easier to complete.
Wolfdogs appear in the snowfield when Sniper Wolf dies. They are not present in the original, at least on Disc 1 (after switching to Disc 2, heading back to the snowfield will reveal a wolf pup in place of Wolf's body).
The spotlights on the helipad sweep vertically, in the original, they swept horizontally.
The locker inside the Nikita missile storage area of the B2 Armory has a poster on the inside of the door that depicts the main antagonist of Eternal Darkness, Pious Augustus.
The final section of the battle with Gray Fox, in which Fox generated an electromagnetic field for the player to avoid, was removed.
Many small modifications were made to level layout and design. For example, figurines of Mario and Yoshi are now found in Otacon's office, along with a GameCube and a wireless Wavebird controller. Shooting Mario will also slightly restore life.
There is now a drainage duct running along the width of the canyon, which Snake can crawl into and hide in.
In the original version, there is a PlayStation on one of the desks in Otacon's office. In The Twin Snakes, it is a GameCube.
Disposal hatches were added near the cliff of the heliport.
During the torture sequence, Revolver Ocelot will now only electrocute the player 3 times, regardless of the difficulty level they are playing on.
The top of Metal Gear REX's head (where the player fights Liquid Snake) is noticeably bigger as compared to the original, making it so that the rail gun protrudes out so much that it actually hits the wall located beneath the control room.
Sentries patrolling the warhead storage building are armed with shotguns fitted with knock-out rounds, which makes more sense from an in-universe point of view (Snake cannot use weapons in this area so as not to damage the warheads).
When Snake has to escape from the Hind D at the top of Comm Tower A, the player may choose to hang-drop all the way down if they did not grab the Rope item.
In the Psycho Mantis fight, Snake now has more time to look around in first-person before the view switches to Mantis' POV. In addition, occasionally during the battle, Mantis will use his psychic abilities to have the room "tilt," alluding to one of the sanity effects from Eternal Darkness.
Right after entering the Comm Tower, Snake was originally spotted by a camera. In The Twin Snakes, he trips an infrared sensor (introduced in Metal Gear Solid 2).
To beat Psycho Mantis, the player must periodically go through all four controller ports as Mantis begins to recover the ability to read Snake's mind, as opposed to the original two.
The layout of the catwalks in REX's hangar was revised, with overhangs being removed or rearranged, such as the PAL key temperature shortcut, and ladders being replaced with stairwells. Also, loading times between levels have been removed, and the player is no longer able to climb over REX's head since the ladders have been removed.
At the cliff of the heliport, a railing has been added; in the original, Snake would be blocked by an invisible wall.
The camera is now looking down upon Snake during the rappel section, where the original looked up at Snake.
The lasers in the Tank Hangar can now be destroyed by shooting at the control units next to the lasers (the boxes were introduced in Metal Gear Solid 2).
Kenneth Baker's corpse remains in the armory for the rest of the game after he dies, unlike in the original version.
The M1 tank stays in the Canyon after Snake destroys it, where it was originally gone after Snake went back out to get the PSG1.
The amount of gun cameras in the area before the REX's hangar went from 12 to just 2 on the wall above the door.
The layout of some of the rooms in the armory, heliport, and tank hangar have been slightly altered. A good example is the room where the player gets the FAMAS in the armory. Originally, the room was mainly empty except for the lasers and the FAMAS, but now there are crates in the room.
There are now only 4 cubicles (instead of 5) in the office on B1 of the Warhead Storage Building. The missing 5th office has been replaced with a row of lockers.
Gun cameras can no longer be destroyed by the Nikita in the gassed hallway.
Naomi's Codec call where she explains her motives for FOXDIE before being subdued was moved from the freight elevator in the PlayStation version to right before returning to the control room to input the final key.
While it was possible (though tricky) to defeat REX's second form using the PSG1 in the original, the second form is completely immune to everything but stun grenades and Stinger missiles in the remake. REX also has several new spots which can be targeted to disable some of its weaponry, though hitting these does very little damage to REX itself.
All cutscenes were re-rendered, most undergoing major reworking under guest director Ryuhei Kitamura, including controversial changes such as Snake springboarding off a missile that Liquid fires from his Hind D, launching him into the air where he fires the coup de grâce at Liquid. Minor dialogue changes were made in some areas, which are more closely related to the original Japanese script. They were then implemented in the reminiscing sequences of the Shadow Moses level in Metal Gear Solid 4.
In the original Metal Gear Solid, the first surveillance camera the player encounters will have Snake say, "A surveillance camera?" The delivery of the line makes it seem like Snake was actually surprised to see one. In The Twin Snakes, the line was changed to "A surveillance camera...", with the delivery being more of an observation.
The cutscene in which two soldiers discuss "another" intruder having killed three of their comrades only occurred if the player had been spotted prior to entering the air ducts. However, this dialogue appears regardless of the player's actions in the The Twin Snakes. Similarly, how the first soldier's reaction to the discovery of another intruder differed slightly. Originally, he simply asked "Really?" In the remake, he processes to turn around rapidly and aim his FAMAS as if he's startled by an unseen presence before asking the same question.
The flashbacks to the aftermath of Revolver Ocelot's botched torture session and Decoy Octopus' death are now displayed in sepia tone. In the original game, they were given in present day colors.
In the original Metal Gear Solid, Snake simply says "Damn!" when Baker reveals that he forgot Meryl's Codec frequency. In The Twin Snakes, Snake becomes furious, which eventually leads to him pointing his gun at Baker.
Psycho Mantis's first "appearance" (the result of psychic feedback to Solid Snake shortly after he possessed Meryl), was altered somewhat: in The Twin Snakes, Meryl, shortly after being possessed by Mantis, fired some rounds at Snake, with Snake narrowly dodging them. Mantis then proceeded to rise up with the elevator Meryl was currently on. Originally, Mantis simply disappeared in a flash after this. A similar trick to the one shown in The Twin Snakes rendition would later occur in Metal Gear Solid V: The Phantom Pain with Tretij Rebenok.
An extra scene of Snake tripping the air lock security system in the Tank Hangar was added if the player walks through the security laser beam.
In the cutscene before the battle with the M1 tank, Snake is blown back into a wall by a blast from the tank, then blown forward when the tank shoots at some nearby oil drums. In the original, Snake is blown back by a shot from the M1 tank, but is able to recover in mid-air. Also, the conclusion of the battle was partially changed: originally, the tank exploded immediately after Snake managed to finish off the second tank gunner, one of the Genome Soldiers was also ejected from the tank, and was killed in the impact when Snake approaches his body to get the Lv. 3 card key. In the remake, Snake unpins the grenade and plays self-catch with the grenade when the tank's turret turns toward him. He then throws the grenade into the barrel of the tank turret and walks away. Vulcan Raven then opens the ammunition hatch to discover the grenade inches from the entrance, and recoils and looks away in shock. The tank then detonates the precise moment the pin falls to the ground. Also, the Genome Soldier who was ejected from the tank was briefly knocked unconscious from the impact and was ablaze, but quickly regains consciousness and starts comically patting himself down quickly in a failed attempt to put out the flames on him and attempts to punch Snake, only for Snake to deliver a punch towards his face, knocking him down and subsequently putting out the flames before retrieving the key card from his body.
A whole new cutscene has been added of the Ninja killing all of the soldiers in the hallway outside of Otacon's office. In the original, most were not seen getting killed, only heard, and most were dead by the time Snake arrived in the hallway. On a related note, the soldiers in the cutscene, and to a lesser extent, the gameplay, were also changed to resemble the light infantry instead of the NBC variant.
The part of the gameplay when Snake has to look in the different bathroom stalls to locate Meryl is now an entire cutscene. Requirements for the Meryl Easter egg remain unchanged.
Mantis, prior to fighting Snake, caused the latter to hallucinate that the entire Commander's Room was set ablaze, only for Snake to resist it. A similar trick to The Twin Snakes occurred in The Phantom Pain with the younger Mantis, only in this instance, the flames that occurred were implied to be real.
The aftermath of the Hind battle was extended: Snake apparently wasn't able to score a damaging enough hit on the Hind chopper, to which Liquid then overconfidently fires missiles at Snake. Snake backflipped to avoid the first missile, but then proceeded to springboard onto the remaining missile, jumping high in the air and then firing another Stinger missile at the Hind, landing a crippling blow on it. It should be noted that Liquid's remark right before launching the missiles, "Eat this!", was initially dummied audio from the original game that would have been used in a similar situation, only during the actual boss fight.
The footage of Policenauts that was shown during Otacon's explanation of anime in the original has been replaced with footage of Zone of the Enders: The 2nd Runner. The cutscene is a seamless transition that bridges two cutscenes that were separate in the original.
Right after entering the Comm Tower, Snake was originally spotted by a camera. In The Twin Snakes, he trips an infrared sensor.
In the original, Snake immediately faints after being hit in the neck by a Genome Soldier. In The Twin Snakes, he looks at the Genome Soldier who hit him before fainting.
Prior to the torture sequence, Ocelot will look directly at the camera when he mentions about not using auto-fire. In the PS1 version, he never looks at the camera at any point.
Gray Fox's rescue inside the prison cell is presented as a brief cutscene.
In The Twin Snakes, Snake managed to completely evade Sniper Wolf's shot when she announced her presence by attempting to shoot him. In the PS1 version, Snake ended up being shot by Wolf, but he managed to be relatively uninjured.
In The Twin Snakes, Naomi's call where she admits to injecting Snake with FOXDIE as revenge, as well as the hints that the injection of FOXDIE itself was of Pentagon orders, was moved to just prior to arriving at the REX hangar's control room. Originally, it occurred on the freight elevator just after Snake heats up the PAL key.
The Twin Snakes presents Gray Fox's death slightly differently. In the original PS1 game, Fox's exoskeleton is able to withstand the first of REX's consecutive stomps, while the second stomp crushes him. In The Twin Snakes, REX utilizes only one stomp, and applies gradual pressure on Fox until his exoskeleton gives way. It wipes its foot on the floor afterwards. On a related note, Fox also briefly impaled REX's radome with his high-PS frequency blade in The Twin Snakes, while in the original, he exclusively used his arm cannon to destroy it.
During Liquid's exposition of Snake enjoying all the killing, a red-toned flashback to Snake killing a few guards was added in (specifically when Liquid remarks "I saw the look on your face. It reflected such vitality."). Originally, the scene did not change at all until Liquid explains the Les Enfants Terribles project to Snake.
The ending cutscenes are presented differently. In the original, Snake and Meryl/Otacon, depending on the ending, are trapped under their crashed jeep when Liquid approaches to kill them, just before FOXDIE kills him. In The Twin Snakes, Snake and Meryl/Otacon get out of the overturned jeep, and it is only after a burst of gunfire from a FAMAS that they realize Liquid is still alive. Liquid also succumbs to FOXDIE much slower: the original game had him die of it almost instantaneously, whereas the remake has Liquid initially collapse, but then get up to his knees and attempt to grab Snake twice, followed by a final staredown, before Liquid finally passes away. The original ending also occurs at daybreak, while The Twin Snakes has it still being nighttime.
In the Meryl ending, Meryl attempts to kiss Snake before Snake's Codec beeps, interrupting the moment. Meryl doesn't attempt to kiss Snake at all in the original.
In the Meryl ending of Metal Gear Solid, Debi Mae West uses the Japanese pronunciation of Otacon's name, "Oh-ta-con." When the game's dialogue was re-recorded for The Twin Snakes, the line's delivery was changed to maintain consistency with the pronunciation used by the other members of the English cast. Also in the Meryl ending, Meryl has eight bandages on her legs, arms, and right hand even though Sniper Wolf shot her three times in her legs and left arm. This was corrected in The Twin Snakes.
Several cutscenes containing real life footage have been altered. This is most notable with Baker's description of how a nuclear threat is much more prevalent than during the Cold War, as the original game had used footage of nuclear warheads being loaded and launched as well as overhead shots of a nuclear missile silo as part of Baker's description, whereas The Twin Snakes used footage of plutonium barrels in a nuclear disposal warehouse, the outside shot of a real life nuclear storage warehouse, nuclear barrels being stacked to great heights, as well as fumes emanating from the grated floor and a caution barrier in front of one of the nuclear waste areas, a brief look at some nuclear warheads in storage, a NBC unit uncovering a plutonium cache from a hole with a radiation detector, and a scientist looking through a generator plant all by himself.
The ending text was rewritten to reflect the year 2003, as opposed to 1998 when the original was released.
Ocelot's post-credits phone call to the U.S. President is now the same regardless of which ending the player achieves. In the original PlayStation version, extra dialogue (concerning Solid Snake being the inferior clone, the President being a third clone known as Solidus, and Ocelot being ordered to place "the woman" under surveillance), is not present in the Otacon ending.