War Arc

The War Arc is a story arc that concerns two or more large-scale factions (city-sized at least) in conflict with one another, with the protagonists being involved somehow. The scale will usually be very epic, with politics usually playing a role. Expect to see a Big Badass Battle Sequence.

See also Rescue Arc and Tournament Arc.

Anime and Manga

 * The Whitebeard War saga in One Piece, especially the Marineford arc, where dozens of incredibly powerful characters from throughout the series clash in a massive conflict between pirates and the government. Interestingly, this one doubles as a Rescue Arc, as the pirates storm marine headquarters to save their comrade  from a public execution.

It's also unusual among both war and rescue arcs for a couple of big reasons: almost none of the main cast are present (the protagonist is there, but none of his True Companions) the hero is actually one of the weaker people on the battlefield, and
 * Since most arcs in One Piece involve the Straw Hats arriving at a new location and getting involved in local conflicts between various factions, war arcs are actually pretty common. Notable examples include Alabasta and Skypiea.
 * The Shinobi World War Arc in Naruto is the most recent example, but it had the Konoha Invasion arc several hundred chapters earlier, which tied in with the Chuunin Exams Tournament Arc
 * Bleach: The five-year long (real time) "Winter War" between the Shinigami of the Gotei 13 and Sosuke Aizen's army of Arrancar, finally ending at the climax of the Deicide arc.
 * The second half of the series is building up towards another War Arc, between the Shinigami and the Vandenreich.
 * The ongoing conflict between the Exorcists of the Black Order and the Millennium Earl's Akuma make up a good portion of the Myth Arc for D.Gray-man.
 * The Arachnophobia arc in Soul Eater.
 * The war between the Kingdom of Midland and the Tudor Empire is the second plot of the Golden Age Arc in Berserk.

Comics

 * The Green Lantern has the Sinestro Corps War (Green Lantern Corps vs Sinestro Corps), War Of Light (7 different Corps against each other) and Blackest Night (everybody against Black Lantern Corps).
 * Chaos War is this for Incredible Hercules
 * Cosmic Marvel has had multiple war arcs in last few years. Annihilation was a war between the Negative Zone and the normal universe, Annihilation: Conquest told the tale of the Phalanx's invasion of the Kree Empire, War of Kings depicted the war between the Kree and Shi'Ar empires and The Thanos Imperative was a war between the normal Universe and the Cancerverse.

Fan Fiction

 * The Vizard Trilogyrevolved around the war between the titular Visoreds and the Shinigami.

Literature

 * Books 21-25 (and beyond?) of the Gor series are focused on the war between the city-state of Ar and Cos, the island Ubarate. Tarl, our protagonist, is on the side of Ar; but Cos won the war...so far.
 * Mercedes Lackey has The Mage War in her Valdemar books.
 * Harry Potter has the war between Voldemort's Death Eaters and the wizards of Hogwarts.
 * The Dresden Files has a massive Myth Arc about the Secret War between Red Court vampires and the wizards' White Council, which breaks out in Grave Peril and comes to an abrupt end in Changes.

Live Action TV

 * Babylon 5 featured the Narn-Centauri war, the Shadow war, and the Earth Civil War.
 * A few Star Trek series mustered some of these into their runs.
 * Season 3 of Star Trek: Enterprise has the eponymous Enterprise racing to stop the Xindi from launching an attack on Earth.
 * Deep Space Nine famously featured the two-year war between the Federation and the Dominion, but it also had the Klingon-Cardassian war and the second Klingon-Federation war (before both sides discovered they'd been played like cheap fiddles).
 * The Star Trek: Voyager writers wanted to make "Year of Hell" a season-long arc, but the executives said no, and it was instead made into a two-parter.

Videogames

 * Mass Effect has the conflict with Saren and the geth in the first game. Notable battles include Saren's attack on Eden Prime (the prologue), the geth besieging the human planet-colony of Feros, the brawl on Saren's headquarters at Virmire, a side-quest that has The Hero attacking several bases to prevent the geth from launching an invasion, and the Battle of the Citadel as the finale.
 * The second game, notably, avoids this from the main plotline, but the possibility of a second war between the geth and quarians is addressed several times. Additionally, the Enemy Civil War between the True Neutral geth and the Always Chaotic Evil heretic geth is brought to light, but we never see the actual fighting take place, and we can end it for good during the Sixth Ranger's loyalty mission.
 * In the Arrival DLC, Admiral Hackett outright states that war between the humans and batarians could erupt, following the destruction of a batarian-occupied system. If true, then Mass Effect 3 would feature the intergalactic war against the Reapers and their Husks, the conflict with the batarians, and the quarians retaking their homeworld from the geth, all going on at the same time.
 * The developers have repeatedly said that Mass Effect 3 is the start of World War II IN SPACE!...
 * Halo has the Human-Covenant war as its Myth Arc, with the Covenant Civil War as a late side-effect carrying over to the finale.
 * A major plotline in The Elder Scrolls V: Skyrim is the conflict between the Imperial Legion and the Stormcloak rebellion led by Ulfric Stormcloak. The player is free to help the Empire quell the rebellion or the Stormcloaks fight off the Legion and have Skyrim become an independent nation.
 * Fallout: New Vegas centers around a war between the New California Republic and Caesar's Legion, with Mr. House serving as a potential third party. You're given the opportunity to support any three of those. That or decide to oppose all three and rule Vegas yourself.

Web Original

 * Red vs. Blue has the "war" between the vastly incompetent or undesirable Reds and Blues, but we barely see any sort of firefights between them (Battle Creek flag zealots notwithstanding), and it's actually just a training scenario used by Super Soldiers; the last detail is kept secret from the Reds and Blues themselves.

Web Comics

 * Order of the Stick has the Battle for Azure City.

Western Animation

 * Avatar: The Last Airbender is about stopping a war that's already going on, sort of making it a series-long War Arc.
 * The Teen Titans spent the near-entirety of the fifth season battling the forces of the Brotherhood of Evil, ending just before the final episode.