(Almost) Every reference and connection to the original MSX games made in the Metal Gear Solid series.
[A thread]

[Pictured here, Iroquois Pliskin from MGS2 and Solid Snake's appearance on the cover of the 1987 original game.]
Gray Fox as a character is inherently a reference to the MSX games, as he appears in MG1, MG2, and reappears as Cyborg Ninja in MGS1.
"Hand to hand."
The entire fight scene with Cyborg Ninja is a reference to the fight in MG2, even Colonel Campbell brings up how Gray Fox died in Zanzibar [Land].
At first Gray Fox used Metal Gear, a weapon, and managed to kill his former lover and almost killed Snake in MG2. In MGS1, Gray Fox changes his ideology, saying that a "fool" uses a weapon, and attempts to defeat Metal Gear REX in MGS1.
Meryl has the old Foxhound logo on her arm.
Additionally, this is the same way Snake met Gustava Heffner in MG2, in a woman's bathroom, while he was working with Foxhound.
Gustava ends up dying from a surprise attack.
Meryl is attacked almost the same way, bringing back Snake's painful memory of Gustava.

"I don't want to see any woman die in front of me."
Decoys in MGSV and fake mannequins in Metal Gear 2. Several rooms in Metal Gear 2 have soldiers standing among fake mannequins to fool Snake.
MGSV Mother Base soldiers wearing red berets, just like the soldiers in Zanzibar Land in Metal Gear 2.
Snake and Colonel Campbell worked with Foxhound in the past, which is mentioned in MGS1's intro and is seen in MG1 and MG2.
The Boss' speech in MGS3 is a paraphrased and morally correct version of Big Boss' speech in Metal Gear 2.
"It's not over yet!"
The same words Big Boss says when he's dying in front of Solid Snake, while Liquid says it to Snake later. Liquid is also a clone of Big Boss, to add insult to injury.
The geographical setting of MGS3 is the same place where Zanzibar Land is in Metal Gear 2. (Tselinoyarsk)
"Do you ever put sweets in your rations?" Cecile asks Big Boss in Peace Walker.
In Metal Gear 2, some of the rations contain chocolate.
(Photo courtesy of Metal Gear Wiki)
Cecile and Holly White share many similarities, notably a headband and blonde hair.
Operation Intrude N313 cassette tape in MGSV, which is the same name of the operation in which Solid Snake infiltrates Outer Heaven.
Venom Snake (Big Boss) moments before his final battle with Solid Snake in MG1. The Diamond Dogs logo in the background even turns into an Outer Heaven logo.
Escorting Eva out of the jungle in MGS3.
Escorting Holly out of the jungle in Metal Gear 2.
Big Boss (Naked Snake) wears a beret in MGS3, which could be a reference to him wearing a beret in Metal Gear 2.
Solidus and Raiden share a similar bond to Big Boss and Snake.
"Can we survive long enough to see the 21st century?" -Big Boss
The same person who died on December 24th, 1999. Only a few days away from the year 2000.
Kazuhira Miller or Master Miller was first introduced in Metal Gear 2, so his appearances in MGS1, Peace Walker, and MGSV are all references to his first appearance.
Dr. Madnar helped make Raiden's cyborg body in MGS4. Madnar also created the TX-11s, the TX-55 and Metal Gear D. Madnar appears in Metal Gear 1 and Metal Gear 2.
Big Mama in MGS4 recounts the events of MG1 and MG2. You can even see screenshots of the two games in the background of the last two images.
Additionally, Metal Gear D is seen in the first image, the Metal Gear in MG2.
Grab bag of random references that are mostly self explanatory.
While Metal Gear 2 ends with a sunset and foreboding music, Metal Gear Solid ends with a sunrise and hopeful music.
To add onto this, MG2 takes place during the day in a location with a jungle and bright colors.
MGS1 takes place at night with a mostly gloomy color palette.
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