With the spread of Tiberium across Earth posing a threat to all non-adjusted life on the planet, Kane was left with no choice but to have the Brotherhood ally with the Global Defense Initiative to work together on a response to contain the resource from spreading and ravaging the planet. This decision proved controversial with certain sects within Nod, who wished to continue fighting against the GDI and were not yet ready to make peace with the organizations. These dissenters, Gideon chief among them, later splintered off and formed the Nod Separatists to continue aggression against the GDI, in contrast to Kane's wishes.
While leader of the Nod Separatists, in secret to most, Gideon was collaborating with Colonel Louise James, head of a radical faction within the GDI that sought to wage war against Kane's brotherhood, in order to take out Kane. Seeking to disrupt the creation of the Tiberium Control Network being worked on jointly by the GDI and Nod, Gideon had the Separatists embark on a systematic murder of the Implants which Kane had entrusted with the activation sequence for opening the Scrin portal. Because of the continued interference of the Separatists in his plans for the TCN, Kane stepped up the Brotherhood's efforts to combat the Separatists and defeat Gideon.
In the penultimate battle between the Brotherhood and the Separatists, the Nod Separatists were defeated and Gideon was captured by Kane. To cement himself as the undisputed ruler of the Brotherhood of Nod, Kane arranged for Gideon's public execution as a show of his dominance. However, Col. James interrupted the execution by sniping Kane (or the Commander in the Nod campaign). What happened to Gideon afterwards and whether his execution was finished is not shown.
Global Defense Initiative