Notice the two "Top-Secret" missions after "Destroy the anti-air emplacements"? You'll have to unlock them by finding all 9 XOF Badges in the main Ground Zeroes mission. The first of them is Déjà-Vu.

NOTE: This guide will not do the scenes in the order they are listed in for the sake of sparing time.

FIRST STEP: The chopper, the surveillance camera, the box and the lights, the blackout, the moai and LIQUIIIIIID.

From your starting point, run straight until you reach the first intersection. To your right is an empty magazine that will come in handy very much later. Run to the right and head towards the admin building.

The chopper:
Granted, I don't think you needed a guide for this one. Jumps straight into view on the helipad.
The cutscene should trigger when you sneak to the little cover to the front right of the helicopter and press V to peek. If it doesn't, you'll have to take another look at the image in the mission info section.

A SURVEILLANCE CAMERA?!

From the helicopter you just saw, head further to the red door to the admin building. You will see a surveillance camera, but don't just run into it, hide behind whatever box suits you and peek. The cutscene should trigger, but beware of the guard! Lure him out with the magazine you picked up earlier and take him out with your CQC skills. If you want, interrogate him for intel on a prisoner's location.

A box... and lights??!

From the surveillance camera, head back to the helipad. You will see searchlights and a box, just like in the original MGS. If you didn't take out the guard behind the surveillance camera, he WILL spot you, and if he doesn't the guy on the wall controlling the searchlights will. To avoid being seen, wait until the searchlights just parted ways and head through- but don't sprint, the noise will attract the guards- just walk through in your semi-crawl-whatever-it's-called (press C/ change stance once) The important part here is that the scene doesn't trigger if you just go through, you HAVE to pick up the box in the middle, which will provide you with moderately useful Smoke Grenades.

Now, head into the main admin building through the furthest entrance-this will drop you off right before the the power generator of the admin building.
To illustrate which entrance you should take, here you have a screenshot:

The blackout

Open the gate and turn off the admin building's power supply, Psycho Mantis will appear and you will be rewarded with one more scene recreated.

The moai

Exit the fenced-in area of the power generator through the gate you are yet to open and break into the van (open the red door with E, but be sure that no guard is nearby). Take the rifle inside, you'll notice the special light it has.
Be sure to pick up the grenades, too.
And yes, there is a hidden "Metal Gear Rising: Revengeance" on the opposite wall when you exit.
But for now, head into the underground tunnel. There, you will find a moai on a desk to your left. Shine the light on it (NOTE: I always did it with the light, maybe just getting near is enough- either way, the rifle is very useful) UPDATE: The light is NOT required!

EXTRA: Go save the prisoner in Paz's cage. Go ahead. I dare you.


LIQUIIIIIIIIIID

Backtrack to the beginning of the helipad, and take the jeep. If you still don't have grenades, enter the van you will see a little further to get some.
Drive the van down the road through the tiny tunnel and the scene will trigger.

A soldier and a tank

Drive all the way to Ground Zeroe's original starting position, avoiding the soldiers along the way, and jump into the pit where you found an XOF Badge earlier. There, you will see a tank. Throw a grenade- it doesn't have to land exactly in the hatch, mind you, but it still has to touch the tank.

This was the final scene. Feel free to head back into the admin buidling to exit and take the MGS Quiz - or stick around and go see what happens when you try to free the prisoner in Chico's cage.


Congrats! You just contracted FOXDIE!


But hey, the FOX Engine will take care of that for you. Thank you, FOX Engine!

This is the only extra SCENE (unless I am mistaken), but not the only little cameo extra- those are mostly cosmetic, but I will describe some in the next section nonetheless.

-The american flag is replaced with a FOXHOUND logo
-Snake will comment on most scenes.
-Call Miller from time to time, he will make some nostalgic remarks (in his MGS1 Voice)


P.S.:
You might have noticed the Kojima Productions logos / Metal Gear logos from the different games on some walls / surfaces. They are what the special light rifle is for, not the moai. Shine your light on them and the logo will appear/disappear.
However, nothing special happens when you see them all, so they are purely cosmetic.

Good job dear reader, you beat Déjà-Vu...
Is not what I'm here to say!

You will have to take the MGS Quiz, and if you get even a single question wrong, it's game over.
If, however, you answer all questions correctly, you unlock extra skins for this mission - Snake will have his PSX body, the Marines will be Genome Soldiers etc... If you beat it on hard, you unlock the Gray Fox skin.

Here are the answers:

NORMAL:

1) MGS1 featured Solid Snake infiltrating which island?
Shadow Moses
2) The remote-controlled missile is known by which nickname?
Nikita
3) Who did you need to call on the Codec in order to save your progress?
Mei Ling
4) The Next-Generation Special Forces who took part in the uprising with FOXHOUND were given what treatment?
Gene therapy
5) On which floor of the Nuclear Warhead Storage Building was Otacon's lab located?
2nd Floor Basement
6) What was the Cyborg Ninja's True Identity?
Frank Jaeger
7) Before being called back into action for the mission, Snake lived in Alaska as a...?
Musher
8) What was the maximum load of the elevator in Communications Tower B?
650 lbs (300 kg)
9) What type of storage media did the ArmsTech president give Snake?
Optical disk
10)What is the title of the ending theme?
The best is yet to come

HARD:

1)What did Snake call Otacon's love for a certain female character?
Stockholm Syndrome
2)When Otacon visited Snake at his cell after he was captured, he gave him what level of security card?
Level 6
3)Which boss character was NOT a member of FOXHOUND?
The Cyborg Ninja
4)What was the name of the studio (later renamed Kojima Productions) that developed MGS1?
KCE Japan
5)Who did Otacon fall in love with in MGS1?
Sniper Wolf
6)How did they censor Johnny Sasaki's privates in the U.S. release of MGS1?
Pixelization
7)Snake attempted to give Meryl a handgun of what caliber?
.45
8)After escaping the base, Snake and Meryl encounter a family of which type of animal?
Caribou
9)In total, how many prototypes of the stealth camouflage did Otacon build?
5
10)What did the "P.A.L." in "P.A.L. Key" stand for?
Permissive Action Link

... you're pretty good!