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you can use a save file before the torture scene to choose to save or not meryl, then go to the end and got the other ending that you're missing, but yeah, the codiname fox and big boss can be a bit troublesome
Also you can have 80 saves, making it very easy to segment.
https://metalgearspeedrunners.com/wiki/doku.php?id=big_boss_rank_requirements
You can find the guide on speedrunning the game here, I just learned these skips two days ago so their not too hard to learn, and it's pretty fun.
https://metalgearspeedrunners.com/wiki/doku.php?id=aezez1
The biggest skips happen in the Cell area, and the Communications tower B.
The cell skip is the easier one to figure out, you crawl half way into the vent backwards, you manually go into first person and look up, and the you let go of the First Person button, and stand up at the same time, you'll then clip out of the level, and you can walk right into the torture sequence room, and skip half the game.
The trade off is you skipped Sniper Wolf 1 and can't use the Stinger missiles due to this, so first make sure you touch the PSG1 before continuing on since you'll need it later "it'll be in your inventory despite not being able to use it yet. As you walk you're way to the Communications towers, you'll get your rank ups from the Tank and Psycho mantis fights, so you'll be able to use the PSG1 by then. You'll also probably want to get the Nikita.
There is another skip you can do during the tower climb with the mandatory alert, that involves laying up against the frozen door and looking at a very specific angle, and taking damage so your hit box touches the load zone and skips past the rope repelling part, but this skip is optional.
Next you'll be in Comb Tower B, you'll be able to walk over the Stinger like the PSG1 but you can't use it yet, so you'll need to do another glitch to skip the Hind D, and the Elevator fight. First you walk all the way down to so snake sees the stairs are broken. this changes the position of the Boxes blocking the way to the top of the tower, and it makes it so the Otacon cutscene will trigger, but we want to skip the Otacon scene by getting rid of the Stinger, and by doing that you'll do the weapons glitch which is a little tricky to do, but you'll get the hang of it after a little while.
to perform the Weapons Glitch you need an explosive to damage Snake when he is laying down, A grenade works fine if you space yourself out enough so you take minimal damage. Before the grenade goes of switch to Chaff Grenades, "stun work too" When Snake is in the damage animation you want to unequip your Rations or cardkey, press and hold First Person, and then mash Directions and other buttons. if done correctly you can then change from equipping the chaff to the Stinger, snake will then have the Stinger equipped but still look like he's holding a chaff. You then want to hold the use button so he holds the chaff until it blows up in his hand, the Stinger will now be used up as if it was chaff ammo and it'll be gone.
Doing this deactivates the Otacon cutscene but you can still get past the boxes to the hind D fight, you want to then go to the roof, but then leave right away, "you can use Gernades to blow up the gun cameras on the way back down." this will reload the areas with the boxes blocking the way again, but now you'll be able to climb on top of them, if you run at them correctly, Then drop down to the left all the way to the bottom of the tower, You can then walk right into Sniper wolf 2, from there you can either fight Sniper wolf 2 normally, or you can use the weapons glitch again, but this time equiping the PSG1 which will let you walk though the barrier that supposed to stop you from walking close to Sniperwolf, and this will skip the entire boss right away.
After that you have to go back and pick up the Stinger again, but the elevator will be working fine so it's no big deal, if you skipped Sniper Wolf 2, you still can't use the stinger until you beat Valkan Raven, but the Stinger isn't nessary to be him anyway, if you picked up the Nikita.
from this point you play the rest of the game normally.
The link I posted has videos of all of this, if you need visuals to help you learn.
https://steamcommunity.com/sharedfiles/filedetails/?id=3069111681
Save the game before boss fights, or at critical moments. Save right as you enter an area to not waste time (since you'll restart at the start of the area). Get the stealth and bandana first. Know what items you need, where they are, move efficiently to them. The L1+R1 quit to main menu makes it easy to reload and try again.
Map another button like R3 to X (I use playstation controls), and set turbo with something like 10ms on it to hold during codec calls to efficiently skip through.
You get 1 ration, I suggest leave it for the end. After you fist fight liquid, there will be 1 ration there to pick up for the final chase scene. I think this is where you'll most want it. So don't use a ration prior to this. You get life replenished after each boss fight. That can help a lot. Also immediately give in to Ocelots torture so you don't waste time, and call Otacon to get you out (ketchup method). Also be sure to grab the body armor (B2 of nuke building, first room on left) while returning from being tortured since then you'll have the right door card.
Only kill the first 3 guards at the beginning with Meryl, let her kill the rest (just run back and forth dodging bullets and avoid the grenades). The Famas with bandana makes Mantis and elevator fights easy (hold square to shoot then X to move while shooting). Stay on opposite side of room from Ocelot, I vote north side to avoid shooting Baker, and chuck a stun grenade and shoot like hell in Ocelots general direction to lock on (I even hang out near the middle and shoot diagonally towards where he like to hide behind pillars). Get one hit then move to avoid his bullets. Rinse and repeat. Chaff grenade along with regular grenade on tank fight. 2nd sniper wolf fight use Nikita missiles behind right side snow bank. Chaff grenades with stingers during Rex first phase, second phase run underneath, have him lose you, shoot cockpit from underneath, rinse/repeat. Liquid fight, learn his patterns, and learn to throw him properly with holding square. Final chase battle, hide behind jeep, then grab first guard choke and drag backwards til you can jump in jeep (to reduce being shot while waiting). Then always know where barrels are and shoot efficiently. Don't waste time since it just gets you shot. You wanna get to liquid section of chase fast.
Learn the game and move efficiently and this can be done with little headaches and can be exciting. The skips like the boba skip are fun, but not absolutely necessary. On my run, I finished with 45 minutes extra and zero rations used.
Good luck.