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In late game PvT its about scouting and control I'll lay out how its supposed to work but it just takes some good control to do and practice.

1. You want to keep your collossi in the back with zealots in the fron.

2. High Templar usage can be done one of 2 ways you can try and have them spread out for a flank but i find they get sniped pretty easy this way. So what I like to do is keep them a little bit behind my army so they don't get EMPd with my zealots. Then what you want to do is storm everything. Storm the vikings and then the bio.

3. Stalkers are not good as a main unit in the composition but you want to have enough about 10-12 to shoot down and finish off vikings that are being stormed.

4. Archons you want them placed behind the zealots and in front of the colossi this will allow the zealots to charge forward and engage the Terran army while the archons sit between the zealots and collossi attacking both vikings and collossi then act as a barrier for the collossi when the zealots start to die.

5. Scouting its really important you take a fight when and were you want to since you need to have your units spread right or a few good EMPs could end you day. so make sure you have good observer placement along with some patralloing zealots running around here and there. When you scout an attack coming spread your units out so the zealots engage first followed by archons and then stalkers and collossi and HT.

6. Again a good spread is crucial zealots in front, Archons Collossi/stalkers, and then HT this allows the zealots to slam into the Terran army keeping them from coming any farther forward and EMPing the back of your army and allows your HTs time to storm the vikings then the bio which during your stalkers are killing off the vikings.

7. With high templar in the late game you need a good amount 7-9 with some spread out for flanks some in the front to get a good pre-emptive storm and the rest in the back to get the assured storms.

8. Basically the way things break down for protoss in late game is like this; Zealots are for pinning and tanking the army, Collossi are for killing the ghost off from afar and aoe, archons are for tanking, stalkers are for vikings, and HTs are your main dmg dealer and are mainly for storms since you will never be able to feedback and trade with ghost cost effectively so DON't try.

From I'm getting from you you have your army clumped together in a ball and its getting EMPed in a clump and thats pretty much it. Try doing what I said above and spreading your units like that while keeping a seperate hot key for stalkers, High templar, and Colossi so you can micro them individually of your main army. late game Protoss vs Terran is all about controll and the first few seconds of the engagement who ever catches the others army in a clump and lands a money EMP or Storm will pretty much win.