Review Detail of Dustypirate009 in Starting With 3000 Special Agents' Protection

Well I don't understand the common sense here. Give him 1 million special agents in secret? Why? According to common sense government would contact such scientist and pay him salary and all things without hiding for such target. I don't find any reason to hide things from MC. The plot doesn't make sense. All plot is doing is creating typical face slapping atmosphere for MC. Well please explain me if I am wrong.