Following the victory at Dakara in which both the System Lords and the Replicators were defeated, the Rebel Jaffa were united as never before, and they set about the task of building a new Jaffa Nation. The holy ground of Dakara became the new homeworld for free Jaffa, and there a great city was erected.
The new nation would be presided over by a High Council, on which both Teal'c and Bra'tac served as interim members, but the struggle to build a whole new system of government that would span Jaffa worlds throughout the galaxy was a difficult one. Many Jaffa were still steeped in an old culture full of antiquated rituals and were slow to accept change. Major Davis and representatives from the SGC attempted to offer guidance, but many Jaffa viewed the Tauri with mistrust and considered the proposed system of government to be a means to control and subvert their newly acquired freedom. Teal'c attempted to be a voice of reason, but his allegiance to the Tauri did not serve him well in winning votes from the most traditional of the Jaffa electorate.
Gerak emerged as a new leader, and his proposed system of government based on military assets found favor among many Jaffa. Teal'c and Bra'tac saw Gerak's rise to power as the corruption of a few power hungry individuals, and they attempted to negotiate with regional coalitions that had yet to declare their allegiance. Nevertheless, a quick vote was taken, and Gerak's motion was resolved by a slim majority. The Jaffa Nation would be ruled by a High Council, the votes of which would be attributed to the various coalition representatives based on military assets. As the representative with the greatest military power, Gerak became the new leader of the Jaffa Nation.
Although Gerak accepted an invitation to the SGC to discuss a treaty with Earth, he dismissed the claims of Teal'c, Bra'tac, and Ka'lel that the Tauri and the Tok'ra had been instrumental in securing the freedom of the Jaffa and should be considered as allies. He resisted any attempt at an alliance, and instead he began steering the Council into distrusting Teal'c for his loyalty to the Tauri. Ba'al had been hiding out on Earth, and Gerak secretly sent a contingent of warriors to Earth to search for him. By capturing and executing Ba'al's clone, he won the hearts of the Council, claiming a big moral victory and reaping the huge political gain that would guarantee him the support of the undecided Jaffa and assure him undisputed influence over the Council.
Gerak used his authority next to bring the Jaffa to Origin, and he proposed to the High Council that the religion of the Ori be adopted by all Jaffa as law. His arguments swayed many, especially the older members of the Council who sought a quick path to ascension. Despite warnings from Teal'c and Bra'tac about the true intentions of the Ori, the Council began to lean toward accepting the proposal, and as Gerak was transformed into a Prior, he was ordered to bring the Jaffa Nation to Origin. The decision nearly brought the fledgling nation to civil war as Bra'tac, Teal'c, and their followers prepared to make a stand against Gerak at Chulak. However, Teal'c dissuaded Gerak from the path he had chosen, and Gerak agreed to come to Earth, where he cured the Prior plague that had stricken thousands, before vanishing in flames.
The Jaffa Nation was left without a leader, and the Council considered a new proposal for a move toward democracy. Strongly in favor of restructuring the government, Bra'tac and Teal'c proposed a referendum to allow all Jaffa to vote for the dissolution of the High Council. The motion to dissolve the Council in favor of elected officials spawned strong opposition from those who had reaped the benefits under the current regime and feared losing their status should a vote for democracy pass. The vote was further hampered by shifting allegiances as Ba'al brainwashed key members of the Council, including U'kin, Maz'rai, and Ka'lel, in order to control the Jaffa Nation himself. Nevertheless, when the vote was taken, the referendum passed, marking the beginning of democracy for the Jaffa Nation. For the first time in their history, leaders would be voted upon by every free Jaffa.
Arrangements were made to hold the first general elections in two months' time, and in the meantime the government was placed in the hands of an Interim Council. The Interim Council cooperated with the SGC in locating and attempting to destroy the Ori supergate, and several Jaffa ha'tak vessels participated in the battle at the supergate as Ori warships entered the galaxy. Faced with the Ori threat, Se'tak, the new Jaffa leader, convinced the Council that their only hope for survival against the armies of the Ori was to use the Ancient weapon on Dakara. Using the device to unmake living beings, Se'tak ordered the attack on several worlds that had fallen to the Ori, and he rejected Landry's insistence that the war with the Ori was not justification for incidental genocide. His strategy was the downfall of his nation, however, for as he fired the weapon at Adria's ship, she launched a counterstrike which left Dakara and its weapon in ruins.
For generations the Jaffa had plotted and fought for emancipation but never planned for what they would do with freedom after it was won. The resulting infighting and weakness after the victory over the Goa'uld led the Jaffa to vulnerability at the hands of the Ori. Without Dakara to unite them, the fractured Jaffa Nation was in disarray, and many reverted back to old warring factions. Parnon, an influential Jaffa leader, organized a peaceful leadership summit at Dar Eshkalon with the intention of organizing a new Council meant to lead the Jaffa and unite them against the Ori. However, the summit was sabotaged by an agent of Arkad who planted explosive devices that killed 32 and wounded 12. Once again the Jaffa factions were scattered, leaving the Jaffa Nation to begin rebuilding once more.