Fidelias said:
But they were just soldiers. Actually, they were soldiers that weren't even following orders. They also hadn't pieced any of it together until after their men started dying. They weren't a threat until Sheperd started killing. Just doesn't make any sense.
While Roach and Ghost are being killed, you can hear Price over the radio yelling to them that they shouldn't trust Shepard, and that he was behind everything. TF141 did figure it out, but only just a second too late. Also, Shepard couldn't be sure they hadn't seen anything in the safe house that might compromise his plan, or that they had made a copy of the data. As for why Shepard would do it himself, the game makes it clear that he isn't the type to let others do all of his dirty work. Heck, the very first mission of the game has him fighting on the front line of a battle, despite being a general.
I might as well take the time to answer some other MW2 "plot holes" people are finding.
1. Pvt. Allen infiltrating Makarov's group and then being killed was part of Shepard's plan. He was planted for the express purpose of leaving an American body at the site of the attack. Shepard had no intention of bringing down Makarov until he was no longer useful, and likewise Makarov had no problem working with Shepard if he got to start a war that killed Americans, who he blamed for Zakhaev's death.
2. Shepard wanted to start a war in order to gain public and government support for the U.S. Military, and to secure a place in history as a war hero. The nuclear attack in CoD 4 had destroyed U.S. morale, turned the public opinion sharply against any sort of military expenditure or involvement, and left Shepard's name forever remembered as "That guy who got 40,000 people killed in a single attack". So he started a war with Russia, with the plan of winning and becoming a hero.