Let's hope that the mystery of time travel is never solved, because a war fought with the tools available through temporal manipulation would make the destruction and death caused by the great wars of the past pale in comparison. A true time war could eliminate entire civilizations: man, woman and child - but without ever spilling a drop of blood, because in a true time war, they would never have even existed.
One of the ongoing memes on Doctor Who has been just such a conflict, the Great Time War, which completely destroyed both the Time Lords and the Daleks,* but in spite of frequent references very few actual details have been introduced. How would you fight a war in - or with - Time?
On an individual basis, time travel would stretch and compress the phenomenon of combat. Soldiers would flicker in and out of battle, taking months to recover from wounds if necessary, then return to the fight only an instant after leaving it. It's not impossible that once the war had started (if it's even possible to use the linear concepts of "start" and "end") there would only be one battle which would make up the entire war.
In fact, you only need one soldier on each side. It would be possible to invest the total scientific and military efforts available into the production of a single perfect soldier armed with every conceivable option for defense and offense, then duplicate them into near-infinity by time jumps to a single destination from multiple points in their timeline**. Roger Zelazny offers this scenario in Creatures of Light and Darkness:
Thirty seconds ago, Wakim is standing behind the General and Wakim is standing before the General, and the Wakim who stands behind, who has just arrived is that instant, clasps his hands together and raises them for a mighty blow upon that metal helm—
—while thirty-five seconds ago, the Steel General appears behind the Wakim of that moment of Time, draws back his hand and swings it—
—while the Wakim of thirty seconds ago, seeing himself in fugue, delivering his two-handed blow, is released to vanish, which he does, into a time ten seconds before, when he prepares to emulate his future image observed—
—as the General of thirty-five seconds before the point of attack sees himself draw back his hand, and vanishes to a time twelve seconds previously….
All of these, because a foreguard in Time is necessary to preserve one’s future existence…
… And a rearguard, one’s back…But do they really need any sort of weapons? At some point, Time itself would become the weapon of choice - no need for explosives or bullets, simply age the enemy out of existence.
In a conventional conflict, armies capture territory. In a time war, victory might hinge on control over eras of history. In Brother Assassin, Fred Saberhagen suggests that in the same fashion that radar tracks enemy missiles, it would be necessary to somehow track the progress of temporal incursions into the past through the time stream, to observe the ripples of change grow to a wave and, when (or if) the threat to history had been eliminated, to watch the wave subside again as events return to normal. Barrington J. Bayley's The Fall of Chronopolis sensibly introduces the idea of an historical archive somehow removed from the standard timestream so that it's possible to map whatever changes the enemy has made. (Because in the standard timestream, the changes aren't changes - they're memories and documented history.)
After all, on a tactical and strategic level, the possibilities are infinite. Ray Bradbury's story The Sound of Thunder suggests that simply crushing a prehistoric butterfly would resonate into the future with unexpected consequences. Taking that as a baseline, consider the effects of detonating a thermonuclear weapon in the centre of Rome during the time of Julius Caesar.
Undoubtedly this would have a massive effect on the time stream, but the problem would be trying to predict exactly what that effect would be. Does nuking Rome help or hurt your cause? Rationally, tactical strikes at an opponent's history would have more of the rapier than the bludgeon in their planning.
The key word in the preceding paragraph is "rationally". The losing side is not always rational, and time war opens horrifying new vistas for the infamous doctrine of Mutually Assured Destruction. A defeated opponent could easily decide to activate some doomsday option that would spell the complete and utter destruction, if not the non-existence, of every life form on the planet. And no need to do anything as obvious as blowing up Rome - all that's required is a carefully placed spoonful of bleach in some primitive pool of amino acids.
And who knows? It's entirely possible that we've already lost.
- Sid
* Well, for the standard TV science fiction series value of "completely destroyed". There are more Daleks still running around than cockroaches in a cheap New York apartment.
** Or multiple destinations from a single point, come to think of it.