KAVANAUGH, Circuit Judge:
This case raises significant questions about the scope of the Executive’s authority to disregard federal statutes. The case arises out of a longstanding dispute about nuclear waste storage at Yucca Mountain in Nevada. The underlying policy debate is not our concern. The policy is for Congress and the President to establish as they see fit in enacting statutes, and for the President and subordinate executive agencies (as well as relevant independent agencies such as the Nuclear Regulatory Commission) to implement within statutory boundaries. Our more modest task is to ensure, in justiciable cases, that agencies comply with the law as it has been set by Congress. Here, the Nuclear Regulatory Commission has continued to violate the law governing the Yucca Mountain licensing process. We therefore grant the petition for a writ of mandamus.
I
This case involves the Nuclear Waste Policy Act, which was passed by Congress and then signed by President Reagan in 1983. That law provides that the Nuclear Regulatory Commission “shall consider” the Department of Energy’s license application to store nuclear waste at Yucca Mountain and “shall issue a final decision approving or disapproving” the application within three years of its submission. 42 U.S.C. § 10134(d). The statute allows the Commission to extend the deadline by an additional year if it issues a written report [258]*258explaining the reason for the delay and providing the estimated time for completion. Id. § 10134(d), (e)(2).
In June 2008, the Department of Energy submitted its license application to the Nuclear Regulatory Commission. As recently as Fiscal Year 2011, Congress appropriated funds to the Commission so that the Commission could conduct the statutorily mandated licensing process. Importantly, the Commission has at least $11.1 million in appropriated funds to continue consideration of the license application.
But the statutory deadline for the Commission to complete the licensing process and approve or disapprove the Department of Energy’s application has long since passed. Yet the Commission still has not issued the decision required by statute. Indeed, by its own admission, the Commission has no current intention of complying with the law. Rather, the Commission has simply shut down its review and consideration of the Department of Energy’s license application.
Petitioners include the States of South Carolina and Washington, as well as entities and individuals in those States. Nuclear waste is currently stored in those States in the absence of a long-term storage site such as Yucca Mountain.
Since 2010, petitioners have sought a writ of mandamus requiring the Commission to comply with the law and to resume processing the Department of Energy’s pending license application for Yucca Mountain. Mandamus is an extraordinary remedy that takes account of equitable considerations. The writ may be granted “to correct transparent violations of a clear duty to act.” In re American Rivers and Idaho Rivers United, 372 F.3d 413, 418 (D.C.Cir.2004) (internal quotation marks omitted); see also Arizona v. Inter Tribal Council of Arizona, Inc., — U.S.-, 133 S.Ct. 2247, 2260 n. 10, 186 L.Ed.2d 239 (2013) (noting that if the federal Election Assistance Commission did not act on a state’s statutorily permitted request, “Arizona would be free to seek a writ of mandamus to ‘compel agency action unlawfully withheld or unreasonably delayed’ ”) (quoting 5 U.S.C. § 706(1)).
In 2011, a prior panel of this Court indicated that, if the Commission failed to act on the Department of Energy’s license application within the deadlines specified by the Nuclear Waste Policy Act, mandamus likely would be appropriate. See In re Aiken County, 645 F.3d 428, 436 (D.C.Cir.2011). In 2012, after a new mandamus petition had been filed, this panel issued an order holding the case in abeyance and directing that the parties file status updates regarding Fiscal Year 2013 appropriations. At that time, we did not issue the writ of mandamus. Instead, in light of the Commission’s strenuous claims that Congress did not want the licensing process to continue and the equitable considerations appropriately taken into account in mandamus cases, we allowed time for Congress to clarify this issue if it wished to do so. But a majority of the Court also made clear that, given the current statutory language and the funds available to the Commission, the Commission was violating federal law'by declining to further process the license application. And the Court’s majority further indicated that the mandamus petition eventually would have to be granted if the Commission did not act or Congress did not enact new legislation either terminating the Commission’s licensing process or otherwise making clear that the Commission may not expend funds on the licensing process. See Order, In re Aiken County, No. 11-1271, 2012 WL 3140360 (D.C.Cir. Aug. 3, 2012).
[259]*259Since we issued that order more than a year ago on August 3, 2012, the Commission has not acted, and Congress has not altered the legal landscape. As things stand, therefore, the Commission is simply flouting the law. In light of the constitutional respect owed to Congress, and having fully exhausted the alternatives available to us, we now grant the petition for writ of mandamus against the Nuclear Regulatory Commission.
II
Our analysis begins with settled, bedrock principles of constitutional law. Under Article II of the Constitution and relevant Supreme Court precedents, the President must follow statutory mandates so long as there is appropriated money available and the President has no constitutional objection to the statute. So, too, the President must abide by statutory prohibitions unless the President has a constitutional objection to the prohibition. If the President has a constitutional objection to a statutory mandate or prohibition, the President may decline to follow the law unless and until a final Court order dictates otherwise. But the President may not decline to follow a statutory mandate or prohibition simply because of policy objections. Of course, if Congress appropriates no money for a statutorily mandated program, the Executive obviously cannot move forward. But absent a lack of funds or a claim of unconstitutionality that has not been rejected by final Court order, the Executive must abide by statutory mandates and prohibitions.
Those basic constitutional principles apply to the President and subordinate executive agencies. And they apply at least as much to independent agencies such as the Nuclear Regulatory Commission. Cf. FCC v. Fox Television Stations, Inc., 556 U.S. 502, 525-26, 129 S.Ct. 1800, 173 L.Ed.2d 738 (2009) (opinion of Scalia, J., for four Justices) (independent agency should be subject to same scrutiny as executive agencies); id. at 547, 129 S.Ct. 1800 (opinion of Breyer, J., for four Justices) (independent agency’s “comparative freedom from ballot-box control makes it all the more important that courts review its decisionmaking to assure compliance with applicable provisions of the law”).
In this case, however, the Nuclear Regulatory Commission has declined to continue the statutorily mandated Yucca Mountain licensing process. Several justifications have been suggested in support of the Commission’s actions in this case. None is persuasive.
First, the Commission claims that Congress has not yet appropriated the full amount of funding necessary for the Commission to complete the licensing proceeding. But Congress often appropriates money on a step-by-step basis, especially for long-term projects. Federal agencies may not ignore statutory mandates simply because Congress has not yet appropriated all of the money necessary to complete a project. See City of Los Angeles v. Adams, 556 F.2d 40, 50 (D.C.Cir.1977) (when statutory mandate is not fully funded, “the agency administering the statute is required to effectuate the original statutory scheme as much as possible, within the limits of the added constraint”). For present purposes, the key point is this: The Commission is under a legal obligation to continue the licensing process, and it has at least $11.1 million in appropriated funds—a significant amount of money—to do so. See Commission Third Status Report, at 2 (Apr. 5, 2013).
Second, and relatedly, the Commission speculates that Congress, in the future, will not appropriate the additional funds necessary for the Commission to [260]*260complete the licensing process. So it would be a waste, the Commission theorizes, to continue to conduct the process now. The Commission’s political prognostication may or may not ultimately prove to be correct. Regardless, an agency may not rely on political guesswork about future congressional appropriations as a basis for violating existing legal mandates. A judicial green light for such a step—allowing agencies to ignore statutory mandates and prohibitions based on agency speculation about future congressional action—would gravely upset the balance of powers between the Branches and represent a major and unwarranted expansion of the Executive’s power at the expense of Congress.
Third, the Commission points to Congress’s recent appropriations to the Commission and to the Department of Energy for the Yucca Mountain project. In the last three years, those appropriations have been relatively low or zero. The Commission argues that those appropriations levels demonstrate a congressional desire for the Commission to shut down the licensing process.
But Congress speaks through the laws it enacts. No law states that the Commission should decline to spend previously appropriated funds on the licensing process. No law states that the Commission should shut down the licensing process. And the fact that Congress hasn’t yet made additional appropriations over the existing $11.1 million available to the Commission to continue the licensing process tells us nothing definitive about what a future Congress may do. As the Supreme Court has explained, courts generally should not infer that Congress has implicitly repealed or suspended statutory mandates based simply on the amount of money Congress has appropriated. See TVA v. Hill, 437 U.S. 153, 190, 98 S.Ct. 2279, 57 L.Ed.2d 117 (1978) (doctrine that repeals by implication are disfavored “applies with even greater force when the claimed repeal rests solely on an Appropriations Act”); United States v. Langston, 118 U.S. 389, 394, 21 Ct.Cl. 506, 6 S.Ct. 1185, 30 L.Ed. 164 (1886) (“a statute fixing the annual salary of a public officer at a named sum ... should not be deemed abrogated or suspended by subsequent enactments which merely appropriated a less amount for the services of that officer for particular fiscal years”); cf. 1 GAO, Principles of Federal Appropriations Law at 2^49 (3d ed.2004) (“a mere failure to appropriate sufficient funds will not be construed as amending or repealing prior authorizing legislation”).
In these circumstances, where previously appropriated money is available for an agency to perform a statutorily mandated activity, we see no basis for a court to excuse the agency from that statutory mandate.
Fourth, the record suggests that the Commission, as a policy matter, simply may not want to pursue Yucca Mountain as a possible site for storage of nuclear waste. But Congress sets the policy, not the Commission. And policy disagreement with Congress’s decision about nuclear waste storage is not a lawful ground for the Commission to decline to continue the congressionally mandated licensing process. To reiterate, the President and federal agencies may not ignore statutory mandates or prohibitions merely because of policy disagreement with Congress. See Lincoln v. Vigil, 508 U.S. 182, 193, 113 S.Ct. 2024, 124 L.Ed.2d 101 (1993) (“Of course, an agency is not free simply to disregard statutory responsibilities: Congress may always circumscribe agency discretion to allocate resources by putting restrictions in the operative statutes.... ”); 18 Comp. Gen. 285, 292 (1938) (“the question with the accounting officers is not the [261]*261apparent general merit of a proposed expenditure, but whether the Congress, controlling the purse, has by law authorized the expenditure”).1
Ill2
We thus far have concluded that the Commission’s inaction violates the Nuclear Waste Policy Act. To be sure, there are also two principles rooted in Article II of the Constitution that give the Executive authority, in certain circumstances, to decline to act in the face of a clear statute. But neither of those principles applies here.
First, the President possesses significant independent authority to assess the constitutionality of a statute. See U.S. Const, art. II, § 1, cl. 1 (Executive Power Clause); U.S. Const, art. II, § 1, cl. 8 (Oath of Office Clause); U.S. Const, art. II, § 3 (Take Care Clause). But that principle does not help the Commission.
To explain: The President is of course not bound by Congress’s assessment of the constitutionality of a statute. The Take Care Clause of Article II refers to “Laws,” and those Laws include the Constitution, which is superior to statutes. See U.S. Const, art. VI (Constitution is “supreme Law of the Land”). So, too, Congress is not bound by the President’s assessment of the constitutionality of a statute. Rather, in a justiciable ease, the Supreme Court has the final word on whether a statutory mandate or prohibition on the Executive is constitutional. See Nixon v. Administrator of General Services, 433 U.S. 425, 97 S.Ct. 2777, 53 L.Ed.2d 867 (1977) (Presidential Recordings and Materials Preservation Act is constitutional); see also Youngstown Sheet & Tube Co. v. Sawyer, 343 U.S. 579, 639, 72 S.Ct. 863, 96 L.Ed. 1153 (1952) (Jackson, J., concurring) (congressional statutes that together preclude President from seizing steel mills are constitutional); see generally Marbury v. Madison, 1 Cranch 137, 5 U.S. 137, 2 L.Ed. 60 (1803).
So unless and until a final Court decision in a justiciable case says that a statutory mandate or prohibition on the Executive Branch is constitutional, the President (and subordinate executive agencies supervised and directed by the President) may decline to follow that statutory mandate or prohibition if the President concludes that it is unconstitutional. Presidents routinely exercise this power through Presidential directives, executive orders, signing statements, and other forms of Presidential decisions. See, e.g., Zivotofsky v. Clinton, — U.S.-, 132 S.Ct. 1421, 182 L.Ed.2d 423 (2012) (based on Article II, Presidents Bush and Obama refused to comply with [262]*262statute regulating passports of individuals born in Jerusalem); Myers v. United States, 272 U.S. 52, 47 S.Ct. 21, 71 L.Ed. 160 (1926) (based on Article II, President Wilson refused to comply with statutory limit on the President’s removal power); see also Freytag v. Commissioner of Internal Revenue, 501 U.S. 868, 906, 111 S.Ct. 2631, 115 L.Ed.2d 764 (1991) (Scalia, J., concurring) (President has “the power to veto encroaching laws or even to disregard them when they are unconstitutional”) (citation omitted); Presidential Authority to Decline to Execute Unconstitutional Statutes, 18 Op. Off. Legal Counsel 199, 199-200 (1994) (Walter Dellinger) (describing as “uncontroversial” and “unassailable” the proposition that a President may decline to execute an unconstitutional statute in some circumstances); 2 The Debates in the Several State Conventions on the Adoption of the Federal Constitution 446 (Jonathan Elliot ed., 2d ed. 1836) (“the President of the United States could shield himself, and refuse to carry into effect an act that violates the Constitution”) (statement of James Wilson).3
But even assuming arguendo that an independent agency such as the Nuclear Regulatory Commission possesses Article II authority to assess the constitutionality of a statute and thus may decline to follow the statute until a final Court order says otherwise,4 the Commission has not asserted that the relevant statutes in this case are unconstitutional. So that Article II principle is of no help to the Commission here.
Second, it is also true that, under Article II, the President possesses a significant degree of prosecutorial discretion not to take enforcement actions against violators of a federal law. But that principle does not support the Commission’s inaction here. To demonstrate why, the contours of the Executive’s prosecutorial discretion must be explained.
The Presidential power of prosecutorial discretion is rooted in Article II, including the Executive Power Clause, the Take Care Clause, the Oath of Office Clause, and the Pardon Clause. See U.S. Const. [263]*263art. II, § 1, cl. 1 (Executive Power Clause); U.S. Const, art. II, § 1, cl. 8 (Oath of Office Clause); U.S. Const, art. II, § 2, cl. 1 (Pardon Clause); U.S. Const, art. II, § 3 (Take Care Clause); see also U.S. Const. art. I, § 9, cl. 3 (Bill of Attainder Clause). The President may decline to prosecute certain violators of federal law just as the President may pardon certain violators of federal law.5 The President may decline to prosecute or may pardon because of the President’s own constitutional concerns about a law or because of policy objections to the law, among other reasons.6 See, e.g., United States v. Nixon, 418 U.S. 683, 693, 94 S.Ct. 3090, 41 L.Ed.2d 1039 (1974) (“the Executive Branch has exclusive authority and absolute discretion to decide whether to prosecute a case”); Community for Creative Non-Violence v. Pierce, 786 F.2d 1199, 1201 (D.C.Cir.1986) (“The power to decide when to investigate, and when to prosecute, lies at the core of the Executive’s duty to see to the faithful execution of the laws.... ”); United States v. Cox, 342 F.2d 167,171 (5th Cir.1965) (“The discretionary power of the attorney for the United States in determining whether a prosecution shall be commenced or maintained may well depend upon matters of policy wholly apart from any question of probable cause.”); Prosecution for Contempt of Congress of an Executive Branch Official Who Has Asserted a Claim of Executive Privilege, 8 Op. Off. Legal Counsel 101, 125 (1984) (Theodore B. Olson) (“the constitutionally prescribed separation of powers requires that the Executive retain discretion with respect to whom it will prosecute for violations of the law”); id. at 115 (“The Executive’s exclusive authority to prosecute violations of the law gives rise to the corollary that neither the Judicial nor Legislative Branches may directly interfere with the prosecutorial discretion of the Executive by directing the Executive Branch to prosecute particular individuals.”); Congressman John Marshall, Speech to the House of Representatives (1800), reprinted in 18 U.S. app. at 29 (1820) (The President may “direct that the criminal be prosecuted no further. This is ... the exercise of an indubitable and a constitutional power.”); see also United States v. Klein, 80 U.S. 128, 147, 13 Wall. 128, 20 L.Ed. 519 (1871) (“To the executive alone is intrusted the power of pardon; and it is granted without limit.”).
In light of the President’s Article II prosecutorial discretion, Congress may not mandate that the President prosecute a certain kind of offense or offender. The logic behind the pardon power further supports that conclusion. As has been settled since the Founding, the President has absolute authority to issue a pardon at any time after an unlawful act has occurred, even before a charge or trial. See Ex parte Grossman, 267 U.S. 87, 120, 45 S.Ct. 332, 69 L.Ed. 527 (1925) (“The Executive can reprieve or pardon all offenses after their commission, either before trial, during trial or after trial, by individuals, or by classes.... ”). So it would make little sense to think that Congress constitutionally could compel the President to prosecute certain offenses or offenders, given that the President has undisputed authori[264]*264ty to pardon all such offenders at any time after commission of the offense. See Akhil Reed Amar, America’s Constitution: A Biography 179 (2005) (“greater power to pardon subsumed the lesser power to simply decline prosecution”).7
The Executive’s broad prosecutorial discretion and pardon powers illustrate a key point of the Constitution’s separation of powers. One of the greatest unilateral powers a President possesses under the Constitution, at least in the domestic sphere, is the power to protect individual liberty by essentially under-enforcing federal statutes regulating private behavior— more precisely, the power either not to seek charges against violators of a federal law or to pardon violators of a federal law.8 The Framers saw the separation of the power to prosecute from the power to legislate as essential to preserving individual liberty. See The Federalist No. 47, at 269 (James Madison) (Clinton Rossiter ed., rev. ed. 1999) (“The accumulation of all powers, legislative, executive, and judiciary, in the same hands ... may justly be pronounced the very definition of tyranny.”); 1 Montesquieu, The Spirit of Laws bk. 11, Ah. 6, at 163 (Thomas Nugent trans., 1914) (“When the legislative and executive powers are united in the same person, or in the same body of magistrates, there can be no liberty; because apprehensions may arise, lest the same monarch or senate should enact tyrannical laws, to execute them in a tyrannical manner.”). After enacting a statute, Congress may not mandate the prosecution of violators of that statute. Instead, the President’s prosecutorial discretion and pardon powers operate as an independent protection for individual citizens against the enforcement of oppressive laws that Congress may have passed (and still further protection comes from later review by an independent jury and Judiciary in those prosecutions brought by the Executive).9
[265]*265To be sure, a President’s decision to exercise prosecutorial discretion and to decline to seek charges against violators (or to pardon violators) of certain laws can be very controversial. For example, if a President disagreed on constitutional or policy grounds with certain federal marijuana or gun possession laws and said that the Executive Branch would not initiate criminal charges against violators of those laws, controversy might well ensue, including public criticism that the President was “ignoring” or “failing to enforce” the law (and if a court had previously upheld the law in question as constitutional, additional claims that the President was also “ignoring” the courts). But the President has clear constitutional authority to exercise prosecutorial discretion to decline to prosecute violators of such laws, just as the President indisputably has clear constitutional authority to pardon violators of such laws. See, e.g., 1963 Attorney Gen. Ann. Rep. 62, 62-63 (1963) (President Kennedy commuted the sentences of many drug offenders sentenced to mandatory minimums); Letter from Thomas Jefferson to Abigail Adams (July 22, 1804), in 11 The Writings of Thomas Jefferson 42, 43-44 (Andrew A. Lipscomb & Albert Ellery Bergh eds., 1904) (President Jefferson both pardoned those convicted under the Sedition Act and refused to prosecute violators of the Act); President George 18 Washington, Proclamation (July 10, 1795), in 1 A Compilation of the Messages and Papers of the Presidents 1789-1897, at 181 (James D. Richardson ed., 1896) (President Washington pardoned participants in the Pennsylvania Whiskey Rebellion).10 [266]*266The remedy for Presidential abuses of the power to pardon or to decline to prosecute comes in the form of public disapproval, congressional “retaliation” on other matters, or ultimately impeachment in eases of extreme abuse.
So having said all of that, why doesn’t the principle of prosecutorial discretion justify the Nuclear Regulatory Commission’s inaction in this case? The answer is straightforward. Prosecutorial discretion encompasses the Executive’s power to decide whether to initiate charges for legal wrongdoing and to seek punishment, penalties, or sanctions against individuals or entities who violate federal law. Prosecutorial discretion does not include the power to disregard other statutory obligations that apply to the Executive Branch, such as statutory requirements to issue rules, see Massachusetts v. EPA, 549 U.S. 497, 527-28, 127 S.Ct. 1438, 167 L.Ed.2d 248 (2007) (explaining the difference), or to pay benefits, or to implement or administer statutory projects or programs. Put another way, prosecutorial discretion encompasses the discretion not to enforce a law against private parties; it does not encompass the discretion not to follow a law imposing a mandate or prohibition on the Executive Branch.11
This case does not involve a Commission decision not to prosecute violations of federal law. Rather, this case involves a Commission decision not to follow a law mandating that the Commission take certain non-prosecutorial action. So the Executive’s power of prosecutorial discretion provides no support for the Commission’s inaction and disregard of federal law here.
IV
At the behest of the Commission, we have repeatedly gone out of our way over the last several years to defer a mandamus order against the Commission and thereby give Congress time to pass new legislation that would clarify this matter if it so wished. In our decision in August 2012, the Court’s majority made clear, however, that mandamus likely would have to be granted at some point if Congress took no further action. See Order, In re Aiken County, No. 11-1271, 2012 WL 3140360 (D.C.Cir. Aug. 3, 2012). Since then, Congress has taken no further action on this matter. At this point, the Commission is simply defying a law enacted by Congress, and the Commission is doing so without any legal basis.
We therefore have no good choice but to grant the petition for a writ of mandamus against the Commission.12 This case has [267]*267serious implications for our constitutional structure. It is no overstatement to say that our constitutional system of separation of powers would be significantly altered if we were to allow executive and independent agencies to disregard federal law in the manner asserted in this ease by the Nuclear Regulatory Commission. Our decision today rests on the constitutional authority of Congress, and the respect that the Executive and the Judiciary properly owe to Congress in the circumstances here. To be sure, if Congress determines in the wake of our decision that it will never fund the Commission’s licensing process to completion, we would certainly hope that Congress would step in before the current $11.1 million is expended, so as to avoid wasting that taxpayer money. And Congress, of course, is under no obligation to appropriate additional money for the Yucca Mountain project. Moreover, our decision here does not prejudge the merits of the Commission’s consideration or decision on the Department of Energy’s license application, or the Commission’s consideration or decision on any Department of Energy attempt to withdraw the license application. But unless and until Congress authoritatively says otherwise or there are no appropriated funds remaining, the Nuclear Regulatory Commission must promptly continue with the legally mandated licensing process. The petition for a writ of mandamus is granted.
So ordered.