Independent branches CANNOT be controlled, influenced by others

Congress is one of the three great and independent branches of the government. It contains the upper house - the Senate - and the lower house - the House of Representatives. This independence from the Supreme Court and the President (also from other commissions and bodies created by the Constitution) is important as the framers of the 1987 Constitution expected, in the words of Justice Antonin Scalia (although referring to the US Constitution from which we patterned and our own), a clash of "power against power."

Separation of powers is basic in our constitutional design. The separation of powers is a fundamental principle in our system of government. It obtains not through express provision but by actual division in our Constitution. Each department of the government has exclusive cognizance of matters within its jurisdiction, and is supreme within its own sphere. (63 Phil. 139; 1936, Per J. Laurel, En Banc)

Even though the Constitution designed a system of checks and balances (A.M. No. SCC-13-18-J, July 1, 2015; Concurring Opinion, Justice Leonen), it must be emphasized that the general rule remains to be separation of powers. Checks and balances can only be done in instances allowed by the 1987 Constitution itself. For example, the Senate sits in judgment of an impeached officer whether the President, a Supreme Court Justice or the Ombudsman. "The Senate shall have the sole power to try and decide all cases of impeachment." (Par. 6, Section 3, Article XI, 1987 Constitution)

Another example is that the Supreme Court is given the power to determine and correct grave abuse of discretion amounting to lack of excess of jurisdiction even on the part of the President or Congress. (Section 1, Article VIII, 1987 Constitution) However, since the fundamental law does not give the Supreme Court the power to interfere with the internal affairs and internal rules of the Senate, judicial power cannot step in. In fact, the Supreme Court, in Arroyo v. De Venecia, held:

It would be an unwarranted invasion of the prerogative of a coequal department for this Court either to set aside a legislative action as void because the Court thinks the House has disregarded its own rules of procedure, or to allow those defeated in the political arena to seek a rematch in the judicial forum when petitioners can find their remedy in that department itself. The Court has not been invested with a roving commission to inquire into complaints, real or imagined, of legislative skullduggery. (G.R. No. 127255, August 14, 1997)

Now that the importance of power separation is clear, it must be emphasized that collusion between two or more branches of government is discouraged because such may be used to deceive the people, perpetrate injustice and accomplish corruption. Blending of powers is good only if constitutionally sanctioned such as when the Commission on Appointments confirms a presidential nominee. (Section 16, Article VII, 1987 Constitution) It may also be allowed in instances that are not repugnant to the Constitution such as when the President suggests a draft of a bill to Congress. ("Presidential Powers." Undated. Retrieved October 02, 2020.)

This is why it is highly improper for any lawmaker, especially the leaders of Congress (the Speaker of the House or the Senate President, most especially), to suggest that they are resigning from post because the President told them to do so. This creates an impression (although not automatically actionable or reviewable via certiorari) that the President controls the Legislature. It is also highly improper for the Chief Justice of the Supreme Court to seek the advice of the President on what the law means or should mean.

The doctrine of separation of powers was also discussed in United States v. Ang Tang Ho, a case which was decided when the Philippines was still under American rule:

By the organic law of the Philippine Islands and the Constitution of the United States all powers are vested in the Legislative, Executive and Judiciary. It is the duty of the Legislature to make the law; of the Executive to execute the law; and of the Judiciary to construe the law. The Legislature has no authority to execute or construe the law, the Executive has no authority to make or construe the law, and the Judiciary has no power to make or execute the law. Subject to the Constitution only, the power of each branch is supreme within its own jurisdiction, and it is for the Judiciary only to say when any Act of the Legislature is or is not constitutional. (43 Phil. 1; 1922, Per J. Johns, En Banc, cited in Justice Leonen's concurring opinion in Mamiscal v. Clerk of Court Macalinog S. Abdullah, Shari'a Circuit Court, Marawi City, A.M. No. SCC-13-18-J, 01 July 2015)

Dissenting opinions in North Cotabato v. Peace Panel (589 Phil. 387 (2008) and in MMDA v. Concerned Residents of Manila Bay (G.R. Nos. 171947–48, February 15, 2011) mentioned that separation of powers entails ensuring that no branch of government shall be controlled or subjected to the influence of another:

Now then, if it be important to restrict the great departments of government to the exercise of their appointed powers, it follows, as a logical corollary, equally important, that one branch should be left completely independent of the others, independent not in the sense that the three shall not cooperate in the common end of carrying into effect the purposes of the constitution, but in the sense that the acts of each shall never be controlled by or subjected to the influence of either of the branches. (G.R. No. 196231, January 28, 2014)