Metal Gear Solid 3: Subsistence .... Help please

If you saved game during the battle with him, then return a few days later (Alternatively you could just change the date of your ps2) you'll get a cutscene of Snake locating End's corpse.

Easiest method:

Run around to the shelter with the SVD inside. When you step out look East of the door. The End usually starts off up there, but can often change positions. 

Goto 'MAP' in the Survival Viewer and enter quickly Up, Up, Down, Down, Left, Right, Left, Right, Square, Triangle.  He'll be the red spot labelled Enemy. Sneak around him and hold him up by aiming your pistol at his head (hold Square) and when he talk, saying he'll never give 'it' you, move your gun away. Aim back at his head, and repeat until he shakes himself down. He'll flee with the aid of a Flash Bang grenade. Pick up the item, Moss Uniform, and wear it along with Woodland face paint in 'Camoflage' in the SV. Repeat the code in a different area to see his position. Line yourself up and keep flicking back to the map (and entering the code, you have to re-enter it each time you leave the Map menu) then head on and aim in his position. When you see what looks like a small sun/mirror-light reflection, try to aim in the middle of that. Bang, you've shot him down his scope. He'll move, so keep entering the code in different regions of Sokrovenno (spelling, I think is wrong)  and lying flat on the ground for high camo index wearing Moss, and in certain areas, 100%.

or you can crawl around for an hour and a half and then snipe him through the eye like i did.

this battle is supposed to be long, but its intense. the best boss battle in the game imo.