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Well we really don't know if the virus killed the guy. We just see him fall on the floor and rash appear on his body. We do know it has the potential to kill because of Eric Sachs comment about the death toll being large. But he also mentions that NY would be under a quarantine and will need his cure, which the government will give him money for it. The money then will help build Shredder empire. The reason why Shredder is doing what he is doing is to rebuild the foot clan to its ancient dominant statis. Shredder to Kari, " The foot clan will rise again. We will reclaim victory." Sachs tell april about an ancient war lord who poisoned the water supply, and an Alchemist who purified the water. Pretty much telling april his scheme, but making himself look like the good guy. Sure it is pretty cliche, but pretty realistic. Ancient warlords just wanted power. If Shredder is a traditional Japanese war lord, there is no reason to give him a deeper reason for world domination. If he is something more then they just left it out for sequel building blocks.
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