Kane died, NOD kingdom collapsed, and GDI forces are resting, thinking the bloody war is finally over. Kane IS dead, this time for real, and his troops are in chaos, but there's one thing GDI didn't count on - CABAL (COMPUTER ASSISTED BIO-ENGINEERED ARTIFICIAL LIFEFORMS).
They didn't shut off the computer, and its intelligence is even greater than Kane's, its thurst for world domination is inevitable, and it has made his database bigger, made a new maps for conquering, invented meaner weapon systems, can't be controlled, can't feel the pain, but CAN unite the Brotherhood of NOD once more.