Not really. The ATS is one of the most apolitical organizations in India. THe problem is, many BJP propaganda often presented terrorism in a "us Vs them" outlook where "us" pertains to law abiding BJP supporters & "them" as dirty, slimy scoundrels from PoK who Congress-I is benefitting. As long as the "them" label fitted a certain religious group, which was not a part of the BJP's mainstream, it suited them well. When a case emerges where one of the BJP's classic golden examples of "US" get involved in terrorism (a podpolkovnik in the Indian Army, and a Sadhvi)- they don't know what to do. And start ranting all these half baked conspiracy theories on an anti terrorism task force, which this country desperately needs.
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From proceedings of the Malegaon case it is apparent that they have been assigned the job to implicate Hindus to prove the theory of their political bosses ie of so called Hindu terrorism. Even a lay man ,leave aside the legal aspects,can judge that they are struggling hard to gather some thing or the other to fix the persons arrested.It appears that they have threatened some media people also who are telecasting ridiculous theories which can at the best be described as unscrupulous.