1. So the whole plot was to erase all the 4 AI right? Is Naomi and Ocelot was on the same boat plotting the same objective, why can't they just do it and have snake to do it in such a terrible way? Poor snake, i almost in tears when i got to keep pressing the triangle n the microwave hallway.

2. At first they mention ocelot was actually liquid manipulating ocelot body from the arm, and in the ending, i heard big boss say is actually ocelot that try to become a doppleganger of liquid to make this mission a success. DId i get it correctly?

3. Big boss, just how big boss got alive? Cause the AI was dead?

4. Zero, just why big boss kill zero?

5. Derbin was the patriot people sent for this mission. And he mentioned that all of them merly & gang, everyone was indirectly sent by patriot for this mission. Who is patriot? Was it the system run by the AI which called SOP? Was the patriot part of the goverment?

6. Now my biggested mystery, got blur from so much plotting in the story. First I understand Sanke got foxdie in the body which will kill him anytime, then middle of the story, he actually got the nanotech in his body as well thank to derbin, and somehow, got mutated to something else which turn him into a walking biological weapon right? THen big boss say something about snake who actually kill big mama and ocelot cause of him foxdie in his body? So is snake going to die or not?

the only thing i can think of is i dont think Snake would've trusted Liquid if he did come clean
other than that,i guess it's just to further the plot.

i loved the split screen.
but yeah,damn sad..everyone fighting a losing battle

several people have different thoughts on this.
some think that in MGS2,Ocelot had Liquid's hand grafted onto his,and Liquid did in fact "infect" Ocelot.
and after MGS2,Ocelot got rid of Liquid's arm and used hypnosis to further make himself believe he is Liquid.

some think that it was never Liquid to begin with.
just Ocelot pretending to be him.

im inclined to believe the latter,but the former does makes sense because we actually hear Cam Clarke(liquid)'s voice in MGS2,and not MGS4

Big Boss was kept alive by the Patriots.
alive and locked away.
the destruction of the AIs released Big Boss from his "prison"/comatosed state.

he says so just before he kills Zero:
"our goal..was to erase zero."
"so long as zero remains,1 will eventually grow to 100 again"

you can take it as a symbolic death,i suppose...since Zero was no longer in charge of the patriots(but the AI was)
so in killing Zero,the founder of the Patriots is gone,and so the patriots wont be brought back to life again.
but as Big Boss said,it's a reboot.
this zero is dead,but a new hope/future has begun.
one which he wants Snake to live in as a man,not a snake

the whole story is about the patriots.
the patriots are kinda like the illuminati.
you dont see them,but they control everything behind the scenes.

the Patriots sent Drebin to help Snake stop Liquid.
the patriots thought that with Liquid stopped,they would be protected.
they didnt count on Snake actually uploading a virus that would wipe them ALL out.

Meryl and rat patrol 01 were patriot pawns.
just that they didnt realise it.

were the patriots part of the government?
they controlled the world.
they were everywhere.

in MGS1 Naomi Hunter infected Snake with the foxdie virus.
it was targeted at certain people only,though and Snake was spared.
in MGS4,the virus has stayed in his body for so long,that it has started to mutate.
maybe his aging quickened the mutation of the virus,i cant remember.
so to counter this,as well as to allow Snake to use weapons in combat, Drebin,under the patriot's orders, infected Snake with a new strand of Foxdie which suppressed his old foxdie and prevented it from mutating even further.
in time the new foxdie would mutate as well.
but Snake only had 6 months to live,anyway before his body gives way.
is Snake dead?
no one knows for sure.
but given that his body had only 6 months to hold out,i guess it's safe to say that he is dead

1. So the whole plot was to erase all the 4 AI right? Is Naomi and Ocelot was on the same boat plotting the same objective, why can't they just do it and have snake to do it in such a terrible way? Poor snake, i almost in tears when i got to keep pressing the triangle n the microwave hallway.
Actually they are all in the same boat, they are trying to defat the Patriots.But they are taking different paths to do it.

2. At first they mention ocelot was actually liquid manipulating ocelot body from the arm, and in the ending, i heard big boss say is actually ocelot that try to become a doppleganger of liquid to make this mission a success. DId i get it correctly?
Yes. In MGS1, Ocelt lost his hand due to an attack by Cyborg Ninja (Gray Fox, Naomi's adopted brother) So in the end of the game, he took Liquid's arm from his corpse and carved it on his own.

3. Big boss, just how big boss got alive? Cause the AI was dead?
Well, to tell you the truth, I thought Big Boss is dead (torched in MG2 Solid Snake) But magically somehow they rebuilt him and kept him under stasis lock as long as the Patriots are still functional

4. Zero, just why big boss kill zero?
Good question. After all the old man is now on two wheelers right? I dont get it at first, but when I realize, this is how Kojima wanted to reboot the series. Zero was the man who started the Patriots. So its from zero, Patriots, then when the Patriots is defeated, its ZEro again. Get it?

5. Derbin was the patriot people sent for this mission. And he mentioned that all of them merly & gang, everyone was indirectly sent by patriot for this mission. Who is patriot? Was it the system run by the AI which called SOP? Was the patriot part of the goverment?
He was not one of the Patriots, he was just one of their henchmen.

6. Now my biggested mystery, got blur from so much plotting in the story. First I understand Sanke got foxdie in the body which will kill him anytime, then middle of the story, he actually got the nanotech in his body as well thank to derbin, and somehow, got mutated to something else which turn him into a walking biological weapon right? THen big boss say something about snake who actually kill big mama and ocelot cause of him foxdie in his body? So is snake going to die or not?
Uh too many questions. Big Mama was killed by fire, not by Snake. And the last question, what do you think? Do you think Snake died/will die?

zero killed for the reason. And the 1 become 2, then 2 become 10 then 10 become 100 part just too confusing to consume... lol

it was their objective.
plain and simple.

to stop Zero by any means necessary.(which eventually led to killing him)

Zero became drunk with power,so they had to stop him.
they couldnt just take him away,his cronies will look for him and eventually save him,and restore him to his almighty position as the head of the state.

so the best and only way to remove him is to kill him.

think of it this way:
Zero is a problem
when that problem starts,you get another problem.
then another,and another...soon you got 100 problems.

much like in the game:
Zero sought to fulfill the boss's wish to unify the world.
then as the head of the patriots,he became drunk with power
eventually he corrupted dr. clark, as well as sigint.
making them his puppets/followers.
later on,not wanting to leave control to his subordinates,creates AI to control the world.
which later went haywire and created the war economy

the only ones not corrupted by Zero's influence are those trying to stop him in MGS4
this is also a problem,as these defectors threatened to destroy the world in trying to stop Zero.
then came the clones who reenacted the very same thing Zero and Big Boss started(naked/solid snake trying to stop a maniac(zero/big boss) from controlling/destroying the world)

Although zero might be the problem, but i do think he know in the end that what he did at first is wrong, well not totally wrong, more like different in idealogy, from big boss ideology. Big boss wanted to free the soldier from becoming the pawn of the goverment, while zero wanted to unite all soldier into one command. As so from what i read, both get the wrong interpretation from the boss herself which lead to today warfare. So i dont think zero really drunk into power, is much more than being wrongly interpreted the will of boss. Although i might be wrong.

Then i dont think he leave all to the AI because he do not want to leave it to the subordinate, he know if he leave it to someone else, the someone will then turn on to misinterprete shi will and make thing more complicated, so he leave it all to the AI to handle it. And yeah, the AI kinda evolve and instead of looping the balance of the world warfare, it become much or fully oriented to war economy.
I think no one try to destroy the world here, as everyone are working at a different aim to either bring freedom, or peace to the world.