Johnson returned to Liberia in March 2004, following the resignation of Taylor as president and the installation of a transitional government. He stated his intention to return to politics, though he briefly left Liberia again on 7 April due to death threats he had received from the
Liberians United for Reconciliation and Democracy (LURD) rebel group. In the
2005 general elections, Johnson contested and won a
Senate seat representing
Nimba County. For a period he served as the chair of the Senate's defence committee. In 2008, Johnson stated that he and Charles Taylor had been solicited to assassinate
Thomas Sankara, naming
Blaise Compaoré as the instigator, with the surety of
Félix Houphouët-Boigny. The investigation conducted since 2015 to clarify the circumstances of this assassination, however, seems to rule out this hypothesis, although doubts persist. In the June 2009 final report of the
Truth and Reconciliation Commission, which was established as part of the 2003 peace deal, the TRC recommended Johnson's inclusion on a list of 50 people who should be "specifically barred from holding public offices; elected or appointed for a period of thirty (30) years" for "being associated with former warring factions." Johnson labelled the recommendation a "joke," noting the absence of several other combatants from the list, and vowed to resist any charges brought as a result of the report. Johnson ran in Liberia's
2011 presidential election as the candidate of the newly formed
National Union for Democratic Progress party. He placed third, with 11.6% of the vote; the election was won by the country's previous president,
Ellen Johnson Sirleaf. Ahead of the
2014 Senate election, Johnson was expelled from the NUDP. Johnson won re-election to the Senate as an
independent. By 2017, Johnson formed a new party, the
Movement for Democracy and Reconstruction (MDR). Johnson contested the presidency with the party in the
2017 election. Johnson supported
Coalition for Democratic Change (CDC) candidate
George Weah in the subsequent run-off election. Weah was ultimately elected president. Towards the ending of 2022, Johnson withdrew his support for President Weah and the CDC. Johnson cited the lack of Nimba County representation in top appointed positions. In December 2022, Johnson resigned as head of the MDR. In an MDR convention on 22 December, Senator
Jeremiah Koung was elected standard bearer. As standard bearer, Koung continued Johnson's policy of opposing the CDC. In the 2023 Senate election, Johnson was re-elected with the MDR. == Death ==