The War is the conflict between Charles Widmore's team of scientists, Jacob's followers, who are loyal to the now dead Jacob, and the Man in Black, who wishes to leave and destroy the Island. It was first foreseen by Widmore, when talking to Locke in Tunisia, and later referenced by the Man in Black, when threatening Widmore after their argument about Jin. After Widmore was killed by Benjamin Linus and the rest of the team were killed by the candidates and the Man in Black, the war was then focused between Jacob's followers and the Man in Black, who was planning to use Desmond to destroy the Island, while Jack Shephard volunteered to replace Jacob as protector of the Island.
With Widmore's death, the war between him and the Man in Black ended, but it would continue with Jack's final stand against the Man in Black. Eventually, Jacob's followers came out victorious after killing the Man in Black.
A team of scientists and soldiers led by Charles Widmore, who came to the Island via submarine in 2007 after being contacted by Jacob. Their ultimate goal is unknown, but it is presumed that their intention was to kill the Man in Black. Most of, if not the entire team, is now deceased, having been murdered by the Man in Black, while Widmore himself was killed by Ben. ("The Candidate") ("What They Died For")
The team consisting of most of the survivors left on the Island, as well as the remaining members of Jacob's bodyguards. Formerly led by Ilana, and afterwards led by Jack following his ascension to protector of the Island. ("What They Died For") They eventually defeated the Man in Black in the final Battle for the Island, but Jack was almost killed during the battle, and ultimately sacrificed himself to restore the Source. He was then succeeded by Hurley, who took Ben as his advisor. ("The End")
A mixed group of survivors of the crash of Oceanic Flight 815 (some of whom also survived Ajira Flight 316) and Others, recruited by the Man in Black. It seems that there are also about 15 unnamed Others currently following the Man in Black. This group is antagonistic to both Jacob's followers and Widmore's team. Most of the Man in Black's supporters were either killed or fled in a mortar attack that effectively started the War and the survivors that the Man had swayed left his side after he attempted to murder the candidates, leaving him alone until he recruited Ben. Ben however, doublecrossed the Man in Black and eventually helped Jacob's followers overpower and kill the Man in Black. ("The End")
Widmore foresees a war in ("The Life and Death of Jeremy Bentham").
Because there's a war coming, John. And if you're not back on the Island when that happens, the wrong side is going to win.