This is part 5 of the MGS4 walkthrough.
Ship's Bow
As soon as the mission starts, run to the right, until you reach the wall, then take out some sort of scoped weapon. If you look to the top left of your screen, you should see a FROG jump from the roof to the top of a flight of stairs, shoot it in the head. Then, depending on what difficulty, you're playing on, one or more FROGS will drop down, shoot them in the head, then run forwards. As soon as you've rounded the big crate, you should see a narrow corridor with explosive barrels to the right and a ladder on your left, ignore both of these things and start crawling along the ground, make sure your octocamo changes, this should give you around 90% camouflage. More FROGS will be in the next area, shoot them in the head. More will drop down, shoot them in the head. Run forwards till you get to a big barrel on your right, wall press past the barrel, then start crawling and take out a scoped weapon. FROGS will be at the end of this corridor thing, shoot them in the head. Run to the end of the corridor until you can't go any further. You will notice a Gekko guarding the door you need to get into, ignore it for now, instead take out the sniper atop the large tower. The USS Missouri will destroy the gekko guarding the door. Once it has been destroyed, wait for the other Gekko to come check it out, then run and open the door, run straight into the elevator and you're done.
Command Center
All you have to do is here is kill/tranquilize the FROGs. There will be many of them, so make use of the computers and walls around you to take cover. Stay on the walls of the room so you will not get shot from behind. Watch out for the ones sniping you from the balcony. Use a 200 round machine gun or P90 if you have one, it makes it much easier, and watch out for the snipers.
Screaming Mantis
After defeating all those FROGs, the final member of the Beauty and the Beast Unit arrives – Screaming Mantis. The battle reeks of the battle with Psycho Mantis in Metal Gear Solid, just don't try to change your controller port!
If you talk to Otacon, he'll guess she's using people's nanomachines to take control of them. Notice you can't aim at her. The gun keeps getting nudged aside... Use the Syringe on yourself.
1. She makes the FROGs shoot at you.
2. She makes Meryl shoot at you.
3. She makes Meryl shoot herself.
Use a CQC chokehold on Meryl, and inject her with the Syringe. Or blast her with a shotgun with V-Ring Air rounds chambered. Note CQC moves that usually knock enemies out can still be used on Meryl.
Keep shooting Mantis, but notice that she takes no damage, but when you hit one of the dolls, she buckles in pain. You need the Mantis doll, but the Sorrow doll is a nice trophy. You need to shoot it around 4 or 5 times before she will drop it, and when she does, hurry to grab it. Keep an eye on the FROGs and deal with them when they're too close, Screaming Mantis will also attempt to attack you with a swinging move which you can dodge by rolling quickly away from her.
Shoot her once with the Mantis doll and shake the SIXAXIS to kill her Beast form. It doesn't count as a kill, so don't worry if you're aiming for a No-Kill Run.
Screaming Beauty. This fight is the same as the other Beauty fights. The Screaming Mantis doll is in the doorway you came from. Collecting all the dolls unlocks the Solar gun. Screaming Beauty facecap is yours if you defeat her non-lethally.
Missile Hangar
There will be Scarabs for the next few rooms, so use a chaff grenade and run through the hallway. If any of them grab Snake, just do a forward roll and keep on going. You can mow down a few to earn some Drebin Points, but there's no point in trying to kill them all: they just keep on coming. If you want to buy any discounted weapons for your next playthrough, now is your last chance!
Next, you will have to make Snake suffer through the hallway of microwaves. All you have to do is keep pressing 
when it tells you to and force Snake to the end of the hallway. This is possibly one of the most touching and heart wrenching scenes in the whole Metal Gear Saga...
Ship Exterior
The final battle with Liquid Ocelot is here after the long cutscenes. Instead of shooting him, you will face it off with a good old fist fight. Only a fool trusts his life to a weapon! The battle is split into four parts. If you die in one of the later fights, you'll have to start at the beginning.
Some general tips for this sequence:
- Use L1 to block Liquid's attacks if he gets close. Some attacks will break your guard, however most of the time Liquid doesn't capitalise on this advantage. Blocking decreases your maneouverability, but also increases your survivability, so learn to love it.
- While blocking you can press R1 for a strong punch, it will hit Liquid off his feet but not that much damage and is a good guard break if a normal combo follows after. You can do 2 strong punches in a row, in case the first one misses or breaks his guarding stance.
- You can sidestep/lunge forwards/backstep by holding various directions and then tapping X (whilst not blocking). This comes in handy to dodge certain moves. You can also tap R1 while lunging to do a guard-breaking uppercut although sometimes Liquid will be able to block it.
- As with the rest of the game's CQC, experiment with different ways of pressing R1. Try holding it or tapping it repeatedly, or pressing it while holding other buttons/moving certain ways.
- Finally, a trick to this battle not mentioned anywhere in the game is that when Liquid taunts you throughout the first three stages of this fight, holding the Triangle button will cause both of your Life gauges to increase, however yours will increase slightly faster than Liquid's. This is paramount to winning the battle on Big Boss Hard/The Boss Extreme (in which Snake will taunt as well).
- You are able to CQC Liquid in all phases of the fight, although CQC wastes time (when doing speed runs, although it will make the fight more interesting) and slightly weaker, it's safer and you are more sure in landing blows on Liquid (although it's less useful in The Boss Extreme)
Liquid
This fighting is similar to how you fought Liquid Snake in MGS and is the easiest of the three fights. A good tactic to use is to corner Liquid and repeatedly hold L1 and then press R1 for a strong punch. If you do this correctly, you will keep attacking him before he even gets a chance to hit you, saving your life for the next fights.
Liquid can and will also interrupt your 5-hit combo after the first kick, especially on higher difficulties. The easiest way to deal with this is to press R1 four times and then hit X to duck out of the way of his counterattack - however feel free to experiment with this battle; part of the fun is figuring out just how many ways you can kick Liquid's butt.
Liquid Ocelot
Now Liquid Ocelot's attacks are much stronger and similar to the second phase when fighting Liquid in MGS1 he's much more active, so be careful of when he unleashes a really powerful punch that can take out 1/4 of your health. He does telegraph this move somewhat, however it often comes while you're in the middle of something else, and there's only just enough time to sidestep it, so unless you see it coming or are already out of range it can lead to a very fast defeat. This fight is much tougher than the first one, so be careful near him. A good tactic to use is after he uses his powerful punch, use CQC against him by holding R1 near him or use the dash attack by pressing 
and then R1. Then, stay some distance from him so that he will do the powerful punch attack again and repeat. Remember to watch out of his normal combo as Liquid can throw it out anytime without you knowing.
Ocelot
For the third fight, it is a CQC brawl. Hence, you can expect Ocelot to use a lot more CQC than you ever want to think about. You can also CQC him (although he can counter your grab attempts), or just beat the crap out of him the old-fashioned way. But be warned, if you get too close to Ocelot, he can headbutt you, which is not only unblockable, but can also deal a great deal of pain. Occasionally Ocelot will grab you in a chokehold. It is recommended that you do nothing during the chokehold sequence at least once, if only to see what happens (don't worry, you won't get a Game Over). Otherwise, just flick the left stick back and forth as prompted to escape, your stamina bar will reduce when Ocelot is choking you according to what difficulty you are playing so watch out in higher difficulties. Alternatively, when given the prompt, use the triangle button to treat him to a nice elbow strike to the kidneys.
He can also do a different CQC and give a hard punch behind your head, although this is much more easier to counter against. Note that Ocelot will block more aften as well and sometimes throws you to the ground (when throwing to the ground it does no damage) and attempts to slam his fist onto you when your down, however it's relatively easy to dodge.
After finishing this fight, both Snake and Ocelot will have become almost worn out and you'll have a final easy fight, where all you have to do is press R1 after approaching near him, eventually ending Ocelot's life, completing the game. Once and for all. Be careful, though, as it is possible to die during this section of the fight.
Now sit back and watch the long, but well deserved ending!
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