An outspoken critic of the administration of President Álvaro Uribe Vélez (2002–2010), she was twice investigated by the Inspector General, which resulted in her being stripped of her seat in Congress in 2005 and again in 2010 and being banned from holding public office for 18 years.

[6] Córdoba was judicially denounced for treason under Colombian law after making controversial declarations against the government and president during a political event in Mexico in March 2007, a charge investigated by the Supreme Court.

In 2010, Córdoba spoke before the European Parliament, asking it to pressure the government of President Juan Manuel Santos into entering into peace talks with the nation's insurgent groups.

She promoted debates focused on minorities and communitarian groups of mothers, as well as the resolution of the Colombian armed conflict through peaceful negotiations.

After 14 months in exile and reports by Colombian authorities that security had improved, Córdoba returned to Colombia to resume her political duties, leaving her family behind.

[citation needed] In the elections of 2002, the regions where Córdoba had traditionally received strong voting results like Medellín and Chocó were seen as being under the control of the AUC paramilitary group.

She then promoted the leftist radical wing of the Colombian Liberal party in order to prevent it from moving towards the political current of President Álvaro Uribe.

For this reason, she founded the Poder Ciudadano Siglo XXI [es] political movement as an internal dissidence of the Liberal party.

Córdoba generated controversy after declaring that "the progressive governments of Latin America should break their diplomatic relations with Colombia" and also that Álvaro Uribe was a "paramilitary".

On 16 August 2007, in a surprising move, President Álvaro Uribe appointed Córdoba as mediator in the humanitarian exchange in an effort to negotiate the freedom of some 50 (number at the time) hostages held by FARC and the possible release of some 500 guerrillas imprisoned by the government.

On 22 November, President Uribe ended the mediation after Chávez broke with diplomatic protocol by placing a series of calls directly to the high command of the Colombian military.

Chávez initially accepted the decision but afterward reacted by pulling his ambassador from Bogotá, and he decided to cease diplomatic relations between the two countries and even announced his intent to sharply reduce bilateral commerce.

This accusation sparked a confrontation with Juan Manuel Santos, the Minister of Defense, who had previously been the subject of other allegations made by Córdoba.

Under the codename of "Teodora de Bolivar", allegedly in reference to the Senator, she would be one of twelve people mentioned as part of a potential transitional government set up by the FARC in the event that they seized power in Colombia.

Interpol reported that the Colombian government had not manipulated the seized computer exhibits and validated their authenticity, but did not certify the accuracy of their contents.

[19] Córdoba claimed the revelations are a "smokescreen" meant to divert attention from the Colombian parapolitics scandal affecting the Uribe administration but Interpol has neither confirmed nor denied the contents.

[21] On 27 September 2010, Senator Córdoba's credentials were revoked by the Inspector General of Colombia, Alejandro Ordoñez, due to her alleged FARC ties.

[22][23] Ordoñez, a conservative jurist, has a track record of using legal pretexts to ban progressive politicians from running for public office, and used similar methods against the mayor of Bogotá, Gustavo Petro.

[23] Based on these and other findings, the Inspector General reported he had established that the senator gave advice to FARC, such as sending voice recordings instead of video footage of the insurgent group's hostages as "proofs of life" in order to improve their strategy.

[23] In 2016, the Supreme Court of Colombia overturned the Inspector General's decisions, ruling that there was insufficient evidence to support his findings and restoring Córdoba's full political rights.