During the first two decades of the 21st Century, the concept of a sovereign form of association has experienced its largest growth since it was first proposed. The 2000s marked the first time that an incumbent governor ran on a platform advocating sovereignty, when Aníbal Acevedo Vilá did so for the Popular Democratic Party (PPD). The term soberanista was popularized as a consequence, and the ideological breach within the party widened as the conservative wing backed the territorial Commonwealth. During the 2010s, free association recorded its best performance at the polls, finishing as runner-up of the 2012 status referendum. This decade also marked the first time that another party presented supporters of free association in the ballot, with the participation of the Movimiento Unión Soberanista (MUS).
Within the PPD Acevedo Vilá, Miranda Marín and the ELA Soberano The perceived inaction of governor Sila Calderón in regards to the political status produced the reaction of several liberal figures within the Popular Democratic Party (PPD), most notably Cordero Santiago. In 2002, José Trías Monge participated in the presentation of a book titled "Crónica de una Guerra Anunciada" authored by Néstor Duprey, where he expressed that there was no perceivable difference between free association as defined by the UN and the culmination of the Commonwealth as envisioned by Fernós.
On May 13, 2002, in expressions directed to president George W. Bush Cordero Santiago stated that "Puerto Rico is a colony of the United States of America and a self-sufficient model can't be developed due to limitations imposed by the executive branch and Congress". At the 50th Anniversary of the Constitution, Miranda Marín insisted that "the goal should be to fight in order to obtain the maximum level of sovereignty possible with double citizenship until we can reach the evolution of our status on that of a Sovereign Associated State in line with the relationship of the countries in the European community". After being jailed for participating in the widespread protests against the presence of the United States Navy in Vieques, Cordero Santiago began organizing a series multi-sectorial reunions with hopes of organizing a new status project based on his belief in free association. However, this was never materialized due to his sudden death on January 17, 2004. Despite being a member of Calderón's cabinet, Acevedo Víla would publicly point out any discrepancy that he perceived with the government's official version, causing a direct confrontation between both. Calderón ultimately supported Hernández Mayoral as the next candidate for the position of governor. Despite this support, Hernández Mayoral abandoned the candidature and former governor Pedro Roselló became the PNP's candidate. Acevedo Víla became the PPD's official candidate, choosing conservative Roberto Pratts as his candidate for Resident Commissioner. This was a strategy to diminish the differences between both wings, portraying a common goal.
In October 2003, after regaining the presidency of the PPD, Acevedo Vilá reaffirmed his expressions of 1998 and within a year, the organization of a Constituent Assembly to attend the status of Puerto Rico became part of the party's 2004 Program for Government. The PPD's government program once again supported the non-territorial development of the Commonwealth. In the 2004 general elections, Acevedo Víla defeated Roselló, while Pratts lost to Luis Fortuño. In 2005, Acevedo Vilá presented a status bill that would attend the issue and subsequently pursue a Constituent Assembly if the people of Puerto Rico supported a new process. However, after the PNP delegation replaced it with a substitutive proposal that established the Constituent Assembly as only "a possibility", the governor vetoed the project citing that "the [PNP was] trying to fool the country". George W. Bush's administration released a task force report in December 2005. The document was controversial among both factions of the PPD, first because it directly declared that the sovereignty of Puerto Rico lied exclusively in Congress and that any further development within the territorial clause was implausible and secondly, because it listed free association as a variant of independence, despite it being listed separately in the UN's General Assembly Resolution 1514. However, the report does differentiate free association from independence in practice, declaring that both the retention of the United States Citizenship and of free access (travel between countries without the need of a visa) between parts could be negotiated as part of the compact. The inform concludes that among the "constitutionally viable" options, it represents the one closest to the historical "perfected Commonwealth".
Amidst the controversy that followed, the PPD's vice president and president of the PPD Mayors Association, José Aponte de la Torre, noted that the party's ideology should be redefined and reaffirmed his belief in free association. Following the release of the Bush administration's status Task Force, the PPD's Government Board approved a document reaffirming its support for a "dignified association" that was based on the sovereignty of Puerto Rico. Acevedo Vilá assigned Carlos Dalmau Ramírez as his representative before the UN's Decolonization Committee, delivering a speech where he asked for cooperation from the UN's General Assembly in pursuing an exercise of free determination and support for a "non colonial, non territorial" form of association. The governor's statement noted that "like the rest of our people, the [PPD] rejects all forms of colonialism", "[now] more than fifty years after the adoption of the Commonwealth, it is evident that the issue of Puerto Rico's status was not resolved in 1952", also arguing the need for a move towards a "sovereign, association [that included] joint responsibility with the United States". On July 16, 2006, the PPD's General Assembly adopted Resolution No. AG2006-01 which established that any citizen interested in running under its insignia, should compromise with the need to "attend the status issue with out dilation" and support the organization of the Constituent Assembly towards that goal. On July 29, 2007, the PPD's General Assembly adopted Resolution No. AG2007-04, in support of Acevedo Vilá's proposal to raise the issue of Puerto Rico's status to the General Assembly of the UN. Resolution No. AG2007-05 was also approved and it established that the sovereignty of Puerto Rico was "irrevocable" and the cornerstone "of a non-colonial, non-territorial association relationship in accordance to international law".
On April 27, 2008, an Extraordinary Assembly was organized where Acevedo Vilá vividly argued the need for a sovereign development of the Commonwealth in association with the United States. The proposal also established that the specifics of the future association would include the considerations of people beyond the PPD and ordered the party's president to present their demands before the UN. PR Rep. Charlie Hernández presented a resolution that reaffirmed the pro-sovereignty posture of the "non colonial, non territorial" development of the status as proposed in 1998, Programs for Government of 2000 and 2004, the similar resolutions approved in 2006-07 and the Enmienda Vizcarrondo (formerly known as General Council Resolution of November 17, 1990). On May 15, 2008, the PPD's Status Commission adopted the party's Program of Government for the 2008 general elections, which was the first document to introduce the label Estado Libre Asociado Soberano when referring to free association. This Commission was presided by Acevedo Vilá and its executive director was Charlie Hernández. Other members included PR Representatives Luis Vega Ramos and Héctor Ferrer, PR Senators Antonio Fas Alzamora and José Luis Dalmau, as well as non-elected figures Roberto Prats and Hernández Colón's eldest son, José Alfredo Hernández Mayoral. None of which openly rejected the pro-sovereignty language during the drafting process. The proposal was prepared by Miranda Marín and established a timeline that went from the Pronunciamiento de Aguas Buenas to a deliberation supporting the non-territorial and sovereign development that first took place on October 15, 1998, and had been approved in seven consecutive General Assemblies. Afterwards Miranda Marín brought the pro-sovereignty proposal before the Program Assembly, responsible for approving the party's proposal prior to the general elections, where it was approved unanimously.
Soberanistas vs. Hernández Mayoral & Ferrer Following Acevedo Vilá's loss, Hernández Colón began pursuing control of the PPD's leadership by supporting conservative candidates for the party's leadership positions. His candidates revived the proposal of a territorial development of the Commonwealth, also recycling the term "permanent union" when referring to this proposal. This shattered the ties that the party had created with other movements and factions, particularly the more liberal ones. With the conservative wing regaining control of the Government Board, Héctor Ferrer, who has publicly expressed his aversion towards free association, was selected as the party's president. The new president designated José Alfredo Hernández Mayoral to the position of Secretary of International and Federal Affairs, which established Hernández Colón's position as the leadership's official status stance. However, this time the conservative leadership decided to adopt the term autonomistas, a vague name that means "autonomy-supporter" and had been frequently used to differentiate the soberanistas, to describe their faction while claiming that they believed in the "maximum autonomous development of the commonwealth within the territorial clause", but did not believe in retaining the sovereignty of Puerto Rico, instead equating it to independence. While conservatives led by PR Sen. Alejandro García Padilla placed the blame of the loss on the pro-sovereignty discourse, others noted that representatives Carmen Yulín Cruz, Charlie Hernández, Luis Vega Ramos and Luis Raúl Torres, as well as senators Antonio Fas Alzamora and Cirilo Tirado were directly elected, while conservatives such as Colberg Toro entered as a product of the Minority Law to the PR House.
A tug war ensued between both factions, where Miranda Marín warned that if the PPD resisted the change implied by free association, it would become irrelevant as a political force during the 21st century.