After Arias' death in 1988, Endara became a leading opponent of the Manuel Noriega military dictatorship, heading the opposition coalition in the 1989 presidential election.

Though his coalition was judged by international observers as having defeated pro-Noriega candidate Carlos Duque, the results were annulled by the government, and Endara and his running mates were attacked in the streets by the paramilitary Dignity Battalions.

[2][3] Endara went to school in Argentina and to Black-Foxe Military Institute in Los Angeles in the United States,[3] where he was described as being a "brilliant student".

[2] In the presidential election of 1989, Endara ran as the candidate of the Democratic Alliance of Civic Opposition (ADOC), a coalition of parties opposed to military ruler Manuel Noriega.

[6] To safeguard against planned vote-rigging by Noriega, ADOC organized a count of results from the country's election precincts before they were sent to the district centers.

"[5] The next day, Endara and his running mates, Ricardo Arias Calderón and Guillermo Ford, led a contingent of a thousand supporters to protest the annulment of the elections and urge that the ADOC candidates be recognized as the winners.

[9][10] Images of the attacks on Endara and Ford were carried by media around the world, and were credited with building public support in the US for the invasion that would soon follow.

[13] Unlike previous rulers Omar Torrijos and Noriega, Endara appointed only whites to ministerial positions, excluding Panama's large mestizo population and other ethnicities.

In October 1994, the National Assembly passed an amendment abolishing the military at Endara's urging, becoming the second Latin American country to do so.

[13] Arias resigned from the vice presidency on December 17, 1992, stating at a news conference that Endara's government "does not listen to the people, nor does it have the courage to make changes".

[19] In February 1990, the overweight Endara began a hunger strike in the Metropolitan Cathedral to call attention to the nation's poverty and to pressure US President George H. W. Bush to dispense previously pledged American aid.

[18] Among other financial scandals, Endara's wife Ana Mae Diaz was accused of reselling food that had been donated by Italy on the streets of Panama City.

[22] In 1992, Diaz won $125,000 in the national lottery and indicated that she intended to keep the money rather than donating it; the incident was also cited as an example of the Endara's administration's lack of concern for Panama's poor.

Martín Torrijos ran on a platform of strengthening democracy and negotiating a free trade agreement with the US, and was supported by popular musician and politician Ruben Blades.

The marriage received widespread coverage and mockery in the Panamanian press, including a new nickname for Endara, El Gordo Feliz ("Happy Fatty").