The Ninja were always an anti-establishment phenomena. Though Ninja served in a multitude of capacities throughout the ages, even inhabiting the loftiest ranks of the Samurai, the Ninja's allegiance was ultimately to family and clan. The Ninja served principle rather than the hollow forms of political power.
"As a military man, to serve one's country, to serve one's lord, or to die for an ideal is important. But something that transcends this is to protect one's country, protect one's lord, and to attain an ideal. This is the true essence of the warrior, and what flows from there is the real bushido." (Masaaki Hatsumi, Soke)
The philosophy of the Shinobi shares much in common with the modern conservative in that the emphasis of perspective is not on the outward trappings of power but on the essential philosophical elements that impel humanity toward freedom. The Ninja of old pursued their individual and familial liberties by means of kyojutsu, since their milieu of operation was one of oppressive totalitarianism. But always, the Ninja were guided by natural principals and operated in opposition to an overreaching government. Modern conservatives pursue the same objectives but from within a radically different environment. The modern conservative is guided by a refined understanding of natural law and inalienable rights, political theories made precise through the interpretation of Divine Revelation. But, fundamentally, the Shinobi of old and his modern conservative counterpart struggle for the same ends: freedom from oppression in all its forms. This realization is most important in these troubled times, when the freedoms inherent in God's creation are being impinged upon by Godless oppressors. The modern liberal is cut from the same pattern as the ancient Shogun. Both move to expand the reach and to coalesce the power of a centralized government. The modern liberal comes as a wolf in sheep's clothing, using the forms of liberty in a campaign of subtle oppression. The spirit of the Shinobi lives, indeed, in these modern times. It is a Shinobi wind that moves through modern conservatism as it struggles against an increasingly centralized federal government, bent upon the erosion of our natural rights.
"Governments are established to oversee the harmonious interworking of all parts of society, but when the rulers become greedy, hungry for power, or lacking in wisdom, the country is subjected to needless wars, disorder, or civil and economic chaos." Toshitsugu Takamatsu, 33rd Grandmaster, Togakure Ryu Ninjutsu