2 options:
*When you enter the fighting area for the 1st time, save game and quit. Go into the clock settings of your PS2 hardware and set the clock forward a couple of years. Load game.

*Thermal goggles. Look for lens flare. Shoot 3 times in center of lens flare.

If you defeat the end by draining his stamina you will get his gun.

Save your game, go to ps2 settings and set the date/time like 2 years forward then load the game up and he has died of old age.

OR just fight him in the traditional way and follow his footsteps on the ground to the other parts of the jungle and scout the surroundings, you can sometimes sneak up on him too and then just beat him up until he throws the flashbang and escapes, rince and repeat.

Basically it just takes a lot of time if you fight him fair. Like 30+ minutes.

is this clock thing serious because if so that is fucking amazing and i will play this game sometime

I think all of the bases have been covered already so I won't comment on the best ways to actually beat him.  But, I have to add that the bosses in MGS3 are really incredible, especially The End.  Fighting The End without taking advantage of any of the numerous cheeseball methods (save trick, thermal goggles, killing his parrot, sniping him earlier in the game etc) is really intense.

Did anyone else notice that many of the bosses in MGS3 can be beaten much more easily if you use thermal goggles?

There's a couple of methods people didn't go over:

- The End doesn't see through the parrot but the parrot does give away your general position when you get close.  Normally, The End falls asleep after a minute but if there's loud noise (including his parrots squawking) he'll go into caution mode which causes him to look around.

- If you do capture his parrot, set it free.  It'll instantly return to its master and he'll spend a few seconds swatting at it to shut it up.

-The end mumbles to himself which you can hear with the directional thing and he also falls asleep and snores real loud.  The End also loses major stamina over time and recharges it once it gets low by soaking up the sun.  It takes him about a minute to do this so you can blast him while he's charging.

-The easiest method (if you don't want an extended sniper battle) is to equip the shotgun and sneak up behind him.  Hold him up to get his camo then blast him.  When he gets up, he'll move at like... 50 miles per hour and drop a stun grenade.  Position the camera to your back so you don't get flashed and then shoot him again which makes him fall down.  Rinse and repeat and you can kill him in 4 hits.

you need to use the fake death pill. i had to look this up online myself.

At the end of the lake press L2 and use the fake death pill.

use the death pill then revive yourself. ez

HA, Easiest way to kill the end is on an earlier level.
Just after you've waded through a river avoiding drone thingies flying over head and the first place you can get the sniperrifle.
You enter an area and there is a cutscene i think its the one where volgan hits the girl at the docks, The end should be in a wheel chair.
If you snipe him there or the explosive barrel near him, He'll be killed and you wont need to do his boss battle. Instead there will be afew of those black, red hatted soldiers if i remember.