The manhunt for the remaining conspirators continues, but Colfax has primarily concerned himself with military matters and the still-ongoing Civil War. The President's initiative to reconnect with the Union armies in the field has allowed him and his administration to essentially identify three major arenas of conflict.
The first is the eastern CSA, i.e. all Confederate states east of the Mississippi River. It contains the Confederate government, including President Jefferson Davis, as well as three of the four remaining Confederate armies (the Army of Tennessee under Joseph E. Johnston; the Department of Alabama, Mississippi, and East Louisiana under Richard Taylor; and Nathan Bedford Forrest's cavalry force).
The second is the western CSA, centered almost entirely on Texas but including small parts of neighboring states and territories. It hosts the fugitive John Wilkes Booth, as well as the fourth remaining Confederate army (the Trans-Mississippi Department under General Edmund Kirby Smith). Because it has been cut off from the rest of the CSA since General Grant's capture of Vicksburg in 1863, Kirby Smith has been acting largely independently and has taken steps to make the territory self-sufficient, meaning that it is the most economically and militarily coherent Confederate remnant.
The third and final theater is the Union's western territories. These contain no centralized Confederate armies, but federal authority there has been weakened significantly by recent events, and frontier violence has seen a dramatic rise. The region's isolation and underdevelopment means that it would be extremely difficult to restore order if the situation there worsened (not to mention that this would also interrupt the supply of precious metals from California and Nevada, harming the nation's finances).