The second challenge, Suzette Nicolas y Sombilon Vs. Alberto Romulo, et al. / Jovito R. Salonga, et al. Vs. Daniel Smith, et al. / Bagong Alyansang Makabayan, et al. Vs. President Gloria Macapagal-Arroyo, et al., on 2 January 2007, was re-decided by the Supreme Court on 11 February 2009. In deciding this second challenge, Court 9-4 (with two judges who inhibit) ruled that "the Visiting Forces Agreement (VFA) concluded on February 10, 1998 between the Republic of the Philippines and the United States is in accordance with the Constitution ... The decision continued, particularly with respect to the subic Rape case, "... the Romulo-Kenney agreements of 19 and 22 December 2006 are not in accordance with the VFA and the Minister of Foreign Affairs, respondent, is responsible for negotiating without delay with the representatives of the United States the corresponding agreement on detention centres under the Philippine authorities, in accordance with Article V, para. VFA, until the status quo is maintained until further decisions of the Court.  UP professor Harry Roque, an adviser to former Senator Jovito Salonga, one of the petitioners in the case, said in a telephone interview about the decision on the consistency of the VFA. "We`re going to appeal...
We hope to be able to convince the other judges to join the four dissenters.  The United States has used the agreement at least twice to keep the accused military under U.S. jurisdiction.  On January 18, 2006, the U.S. Military retained custody of four soldiers accused of rape while they were visiting Subic Bay during their trial in a Philippine court.  They were detained by U.S. officials at the U.S. Embassy in Manila. This has led to protests from those who believe that the agreement is unilateral, harmful and contrary to the sovereignty of the Philippines.
[Citation required] The agreement has been characterized as immunity from criminal prosecution for U.S. military personnel who commit crimes against Filipinos and treatment of Filipinos as second-class citizens in their own country.   As a result of these problems, some members of the Philippine Congress considered ending the VFA in 2006.   However, the agreement has not been amended. On February 11, Philippine President Rodrigo Duterte announced that Manila would denounce the U.S. and Philippine Visit mission agreement (VFA), an agreement that allows the U.S. military to move to the Philippines. Duterte`s decision was taken in Washington with deep concern about the possible consequences of the Indopapacific Strategy (PDF), which was primarily aimed at countering China`s growing strength. If the VFA ends, what will happen to other military treaties and agreements with the United States? Uncertainty about the future of military cooperation between the Philippines and the United States poses challenges to the Trump administration`s free and open Indo-Pacific strategy. Adm Philip S. Davidson, commander of U.S. Indo-Pacific Command, said, "But our ability to assist the Philippines and their violent fight against this, our ability to train and operate within the Philippines and with the Philippine armed forces, would be called into question without this agreement from the Visiting Forces." The VFA must clarify the conditions under which foreign military personnel can operate.
In general, a VFA deals primarily with legal issues relating to military individuals and property. This may include issues such as entry and departure, tax obligations, postal services or the conditions of employment of nationals of the host country, but the most controversial issues are the civil and criminal competences of visiting staff.