This footage is from my recent MGS3 European Extreme difficulty Foxhound ranking run. This strategy may take quite a few tries to get down, but it's definitely worth it if you're struggling with this fight, and also if you're aiming to get that elusive Foxhound ranking.
When the fight starts, keep your M1911 equipped, immediately aim at The Pain and fire a whole clip into him. If you hit every shot, he will stagger; this will stop him from throwing pheromoness at you, which is important because those hornets can kill you very quickly unless you dive underwater.
Switch to the MK22 and get some headshots off on him; you should be able to get 4 headshots before he uses his hornets to armour up. When he does that, equip a Grenade / Stun Grenade / Smoke Grenade, then throw it at him, and when it explodes, his hornet armour will go away. Make sure you ARE NOT in first person view when you throw the Grenade, as it will most likely miss if you are. Once his armour has gone, you can then get some more headshots off on him.
When the second phase starts, he will already have armour, so quickly throw another grenade to get rid of it, and then make sure YOU ARE in first person view when he sends his Bullet Bees at you, as they don't hit you for some reason then. Keep on with the same tactic; get rid of his armour whenever he uses it, and get headshots off on him when you can.
His attacks include throwing pheromones which makes hornets attack you, he can summon a Grenade, he can summon a Tommy Gun, he has Bullet Bees which he can hurl at you, and he can also teleport across to the platform you're stood on to hurt you. After not too long, he will go down.
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