As a criminal judge Mota participated in cases against military figures and civilians accused of crimes committed during the 1973–1984 civic-military dictatorship. She presided over more than 50 complaints based in the Criminal Court of First Instance of the 7th District. On 9 February 2010, she pronounced sentence condemning former President Juan María Bordaberry as "co-author" of an attack against the Constitution, forced disappearance of persons, and political murder of eleven Uruguayan citizens because: The judge deemed that these were
crimes against humanity, under the provisions of Article VI of the
Nuremberg principles. In supporting her actions under
international human rights law, the judge argued that reference to Law No. 18.831, known as the
Expiry Law, was not relevant to this judgment. Regarding the crime of assault on the Constitution, Judge Mota condemned Bordaberry for leading the
1973 coup d'état by dissolving the Parliament through Decree 464/973, a decision that "the Constitution in no way enabled him to take," according to Mota's ruling. The conviction was based on article 117 of the Criminal Code. This crime, which would be
prescribed after 20 years, could not be tried previously due to the interruption of normal functioning of the
rule of law between 1973 and 1985, and for procedural reasons that hindered the judicial process until 2006. During her time as a criminal judge, she had a difficult relationship with the
Ministry of Defense, due to what she considered insufficient cooperation with the cases she was investigating. On 27 September 2012 she went to Infantry Battalion No. 13 accompanied by witnesses, to perform a visual inspection of the Army's Material and Armament Service. During the visit, she was prevented from taking photos by a supposed order of Minister
Eleuterio Fernández Huidobro. Mota declared that the ministerial authorities were in contempt; finally through an agreement she managed to access the site to take photographs. For her work in the cases of human rights violations during the dictatorship she won the support of social organizations and left-wing parties, but her work also earned her criticism. Mota did not deny her commitment to the search for truth and the restoration of justice, while discounting any association of her actions with party politics. ==Investigation into disappearance of Air Class flight==