It is notable that House Arryn and House Martell both remained neutral in the war, and took no part in the fighting. The powerful House Tyrell declared themselves to Renly. House Tully remained closely allied to House Stark throughout the conflict.
The War of the Five Kings is the principal military conflict in in the lore of this sub. It houses both major deviations that make all subsequent lore possible - namely Theon Greyjoy siding with Robb instead of Balon, and Stannis Baratheon failing to murder his brother Renly.
Course of the War
The War in the Riverlands
After Catelyn Tully seizes Tyrion Lannister for the attempted murder of her son Bran, Tywin Lannister raises an army of 35,000 men, divided into two hosts. Lord Edmure Tully demands the Lannisters explain their gathering levies, but receives no response, and so begins to raise his own in defenese. This is hampered, however, by the raids of Ser Gregor Clegane, sent by Tywin to disrupt the Riverlands, forcing many lords to turn their eyes homeward.
Jamie Lannister and his host descend from the Golden Tooth, smashing the paltry army gathered there and pressing on to Riverrun. Beric Dondarrion and his army, sent to apprehend the Mountain, are surrounded and all but destroyed. Jamie Lannister reaches Riverrun, routing the army gathered there and taking Edmure Tully hostage. Lord Blackwood and many riverlander soldiers take refuge within the stronghold, leading to the siege of Riverrun.
The Wolf and the Lion
Robb Stark and his host descend into the Riverlands. The North splits its army in two, sending Roose Bolton and the foot down the Kingsroad toward the Ruby Ford. Robb and his cavalry cross through the Twins, heading toward Riverrun with their strength bolsterd by Frey and Mallister men.
Tywin Lannister and Roose Bolton face off in the Battle on the Green Fork, which ends as an easy victory for the Lannisters. Tywin discovers, however, that he has been decieved - he learns that Robb Stark is riding on Riverrun, and rather than pursuing the remains of Lord Bolton's army, sets a hard pace to bring his army west.
Robb Stark manages to capture Ser Jamie Lannister in the Battle of the Whispering Wood, and the following night attacks the army encamped around Riverrun. It's a rousing success, breaking the Westerland host and sending the survivors back toward Golden Tooth. Tywin Lannister, hearing of this, and the crowning of Renly Baratheon, retreats to Harrenhall, and sends three raiding parties under Ser Gregor Clegane, Ser Amory Lorch, and Vargo Hoat to set the riverlands afire from the Gods Eye to the Red Fork.
The Rise of the Kraken
Lord Balon Greyjoy - now King Balon IX - launches his invasion of the North. He strikes Moat Cailin, Deepwood Motte, and the Stoney Shore, seizing them for the Isles. Theon Greyjoy, however, refuses to lead his father's men, and instead escapes south, to Riverrun, to meet up with Robb Stark and his army. Dagmer Cleftjaw takes Torrhen's Square, and the western coast of the North bleeds heavily beneath the Ironmen.
The Clash of Kings
Theon Greyjoy arrives in the Riverlands, and brings Robb Stark word of the Ironborn attacks in the North. Unwilling to let this stand, the Young Wolf gives command of the Riverland forces, bolstered by a few companies of Northmen, to Brynden "Blackfish" Tully. He points him to a mountain pass discovered by Grey Wind, and then takes the rest of his men north.
Brynden leads the Rivermen through the pass, circumventing the Golden Tooth and surprising Stafford Lannister's newly raised host. The Westerland army is destroyed, giving the Riverlanders command of the region. While lacking the strength to take Casterly Rock or Lannisport, they instead seize Ashemark, raid along the coast, capture thousands of livestock, and take the gold mines at Castamere, Nunn's Deep, and the Pendric Hills.
In the Stormlands, Stannis Baratheon and his five thousand men lay siege to Storm's End. Renly and twenty thousand horse ride to meet him, and the young Stag askes his elder brother to bend the knee. Stannis refuses, and the next morning, the two armies clash. It is a brief struggle; a core of Stannis' men betray him, handing him over to Renly in exchange for their lives. Renly Baratheon exiles Stannis, and all men still loyal to him, to the Wall.
The Baratheon-Tyrell forces advance upon King's Landing. Lord Tywin Lannister, intent on defending his home from the Rivermen, begins to march west toward the Red Fork. Word arrives, however, of Renly's imminent arrival at King's Landing. Before Lord Tywin can reinforce the city, the Tyrell-Baratheon force besieges it.
Renly Baratheon, hearing of Tywin's presence in Harrenhal, gathers an army of fifty thousand to march out and meet him. Renly divides their forces, taking thirty thousand men beneath the command of himself, Loras, and Garlan Tyrell, and giving Lord Randyll Tarly the remaining twenty thousand. A feint by Tywin Lannister draws them out - and Lord Renly, thinking that Tywin's men were no doubt exhausted from their fighting, sends Randyll Tarly to engage him.
Randyll Tarly does not find him, however - instead Lord Tywin advances upon the army of Lord Renly in the night, his twenty thousand battle hardened men, descend upon the unwary Baratheon host. The Battle of the God's Eye is a horrific slaughter, some twenty two thousand Tyrell men slain or routed in the fighting, hundreds drowning in the God's Eye, and thousands fleeing into the night. Renly and his companions barely manage to return to King's Landing, with Tywin hounding the remains of their army all the while.
The Riverlanders, lacking the strength to conquer much more of the Westerlands, pull back. Their localized raiding never extended far to the south, where a hasitly raised army of ten thousand sits at Deep Den, before making a hard march toward the capital. Word reaches them of Lord Tywin's victory at the God's Eye, and the hopeful Westerlanders march even faster, desperate to meet up with Lord Tywin.
During a fierce storm at Pyke, King Balon Greyjoy falls from one of the rope bridges that connect the towers of his castle. A Kingsmoot is called, and Balon's exiled brother, Euron, returns in time to claim the Seastone Chair for himself. He recalls the remaining few raiders in the North, and turns his attention toward the Reach.
The War Winds Down
Robb Stark is victorious in the North, driving away the Ironborn raiders there. With the aid of the Reeds he manages to circle Moat Cailin and attack from the North, before marching on to the Western Coast to liberate the taken strongholds. He sends aid to the Wall at the behest of his half-brother Jon Snow, and there Lord Commander Stannis Baratheon and the Night's Watch defeat Mance Radyer and his Wildlings in the Battle for Castle Black.
The Riverlanders, home from their raiding in the Westerlands, set out to reclaim the abandoned castles that the Lannister forces took, their previous holding garrisons having all fled to rejoin Lord Tywin's army in his attempt to break the siege on King's Landing.
The Battle for King's Landing proved to be the most horrific in all of Westeros history, with two massive armies facing off against one another. Lord Tywin, having stripped the Riverlands of every man still loyal to his cause, and confident the support of the ten thousand fresh men from the south, and the garrison inside King's Landing itself, decides to meet the Reach in the field, trusting the superior discipline and experience of his men to carry the day, despite the still sizeable difference in the size of their hosts. Mace Tyrell urges a retreat, but Renly will hear none of it - the Baratheon-Tyrell forces form up, and by midmorning battle is joined. Thousand upon thousands perish in the fields outside of King's Landing, the Westerlander's advantages telling early on. Numbers, however, do not favour them, and though the ten thousand reinforcements from the south arrive and join the battle, it is not enough. Within the city itself, no one dares open the gates.
Eventually Lord Tywin is slain, and the Westerlands buckles and breaks. WIthin the walls of King's Landing the Mountain Clansmen, tired of starving, overwhelm the gold cloaks at the Lion's Gate and throw it open for the Baratheon forces. Half of the army presses the routing Westermen, while the other half floods into the now open city, their numbers greatly dwindled.
The Feasting Crows
With the West now truly defeated, and Renly Baratheon in possession of the Iron Throne, the war seems near it's end. Renly orders the execution of Lady Cersei Lannister, though her son Joffery is found dead in his chambers. Tommen, Tyrion, and Myrcella are allowed to live - they are cast into exile across the Narrow Sea.
Hardly had the victors settled into the capital before word arrived from the Reach - the Ironborn had taken the Shield Isles, as well as parts of the Arbor. Much of the Reach's strength immediately marches south, still worn from the battle for the city.
Robb Stark, now fully in command of the North, Riverlands, and the recently sworn Vale, begins to consolidate his rule. Rather than disbanding his men, however, he marches south to Moat Cailin, here held by a nominal force in the name of the Tullys, and sends word to Renly Baratheon that he wishes to meet.
When the Reachmen arrive home they find much of the Western coast aflame, its crops stolen or spoiled, its people put to the sword or taken as salt wives and thralls. They rally once more, the fleets of the Hightowers and Redwynes defeating King Euron outside the Whispering Sound, and forcing him to retreat to the Shield Islands even as the Ironborn holdings in the Arbor and on the coast are retaken.
Euron regroups on the Shield Isles, sending word back to Pyke requesting more men. The Ironborn refuse, however, the machinations of Rodrik the Reader and Asha Greyjoy combining with his recent loss to undermine the rule of Euron Crow's Eye. Before he can abandon his conquests, however, the Redwyne fleet arrives to retake the Isles. In a battle known as the Battle of the Shields, the Ironfleet is broken, King Euron is slain, and the last of the Ironborn are thrown out of the Reach.
With the defeat of Euron and winter swiftly approaching, the Iron Isles find themselves in a precarious position. Asha Greyjoy assumes the Seastone chair with the support of House Harlaw and the house of her husband, the Goodbrothers. Together they come the decision that the only way for the Ironborn to survive the retaliation of the South is to bend the knee to the North. Asha sends word to her brother, Theon, and together they manage to arrange a deal with Robb Stark. The Iron Isles would swear fealty to the North, abandoning all raiding in Westeros itself, and serving as their navy upon the western shore. In exchange, the Starks would broker a peace with the Baratheons.
King Robb I Stark and King Renly I Baratheon did eventually meet, agreeing to peace between their two kingdoms. Renly was known to be furious about the division of Westeros, but with winter upon them, half the continent a smoldering ruin, and the armies of every region but the Vale and Dorne exhausted, there was little to be done.