During his life he held several posts, many coinciding with the European Peninsular War: lieutenant general in the military, secretary and councilor of the Conselho Ultramarino (Overseas Council), governor of Algarve and Governor/Captain-General of the Azores.

In 1807, following the French invasion, under the command of General Jean-Andoche Junot, the Portuguese Cortes escaped to Brasil, at a time of when Stocker was secretary of the Real Academia das Ciências (Royal Academy of Sciences).

As part of a requirement for then-Brigader Stocker, to be reintegrated into the Portuguese military, a letter from the Count of Linhares, then-Minister for the Prince Regent in Brazil wrote: His collaborationism with the French Army and the military incompetency in the Orange War campaigns, were published in História Geral da Invasão dos Franceses (General History of the French Invasion) by José Acúrsio das Neves, resulting in a public polemic.

At the same time, though, Stockler elaborated his Ensaio histórico on the origin and progress of mathematics in Portugal, later published in Paris, that was critically acclaimed by José Silvestre Ribeirão (in Resenha de Litteratura Portugueza) and as an insert in the Annaes das Ciencias.

Both political groups in the Azores were hopeful for his tenure: the Liberals, expected a confirmation of the Pro-Constitutional ideas, and the Absolutists, convinced that his nomination by King D. John VI before the revolution, would guarantee his support for the dominance of the monarchy.

The Absolutists were immediately vindicated when Stockler prohibited political contact with Portugal and requested new members of the administration and judiciary from Rio de Janeiro, ignoring the legitimacy and authority of Liberal institutions in Lisbon.

Capitalizing on the discontent with the governance of the Captains-General, on 1 March 1821, a military revolt in Ponta Delgada erupted, headed-by Noronha and lieutenant João Soares de Albergaria, inspired by civil elements angry with the dominance of Terceira (militarily and economically).

But, the interim government did not lose time and revoked many of the laws that subordinated the island of São Miguel to Terceira, abolishing taxes and annulling orders of Stockler that prohibited contacts with the Liberal continent.

[4] Meanwhile, the Junta Governativa of the Kingdom, established on the continent, recognized the Interim government administration in São Miguel and Santa Maria, and placed Stockler in charge of the remaining islands.

[4] In response, Lisbon ordered the division of the Azores into three comarcas (Ponta Delgada, Angra and Horta) governed by Juízes Corregedores (Judge Magistrates) who among their functions oversaw their treasuries.

On 14 April 1821, a revolution broke out in Angra, inspired by those deported from the Amazonas and those loyal to Francisco António de Araújo e Azevedo, forcing Stockler to take refuge in Praia.

[4][6] The municipal council proclaimed the Interim government under Araújo e Azevedo, but the Liberal cause was not as popular as the rebels assumed: he was shot during a counter-revolution and impaled by bayonets, his body taken in loud macabre procession through the streets of Angra.

Stockler arrived in Lisbon and was immediately arrested and imprisoned in the tower of São Julião da Barra, by order of the Cortes, resulting in a long process in the press, that included debates and ridicule.

As a result, on 10 June 1823, it was concluded that Stockler provided loyal service to the Crown within the legal framework bestowed on him, and his career was rehabilitated, along with that of Bishop Manuel Nicolau de Almeida.

[6] After installed in his position the "new" Captain-General immediately began to persecute the remnants of Liberal government and their sympathizers; there were numerous arrests and expulsions from the island, a reign of terror that paralleled the Castilian invasion of 1583.

The other islands of the archipelago quickly stepped into line; on São Miguel the administration proclaimed their obedience to the King in order to save their newfound autonomy, as did politicians on Faial.

On 24 July 1824, Manuel Vieira de Albuquerque Touvar arrived in the Azores to take up his functions as the ninth Captain-General, and a few days later Stockler left again for an uncertain future.

The second volume of his Obras completas was published in 1826, with eulogies to academics Tomás Caetano do Bem and Pascoal José de Melo (an appendix on the history of the French invasion and press freedoms, respectively).

The absolutist connotation of Stockler brought an implantation of liberalism on his work and wrote Ensaio histórico sobre a origem e progressos das matemáticas em Portugal