The War of the Usurper (as it is called by Targaryen loyalists) or Robert's Rebellion (as it was dubbed by the victors) was a major civil war in the history of Westeros. It saw the ruling Targaryen dynasty displaced from power after 280 years and replaced by the Baratheon dynasty.
In the years preceding the outbreak of war, the actions of King Aerys II Targaryen had become increasingly erratic, believed by some to be the result of spending several months as a confined prisoner during the Defiance of Duskendale. He had grievously insulted his former Hand, Lord Tywin Lannister, forcing his resignation after twenty years of leal and efficient service, and had taken a disturbing interest in fire. Rumour also spoke of his mistreatment of the Queen and a tendency towards cruelty.
In 281 AL, the Year of False Spring, the king and his son, Prince Rhaegar, attended a great tourney at Harrenhal. Prince Rhaegar overthrew all challengers but surprised everyone when he named Lyanna Stark of Winterfell as the Queen of Love and Beauty, rather than his own wife, Elia Martell. It appears that Rhaegar became obsessed with the young Stark girl, and the following year he 'kidnapped' her from her family and took her south.
Brandon Stark, the eldest son and heir to Lord Rickard, immediately rode to King's Landing to demand Rhaegar explain himself and return his sister to him. Rhaegar was not present, but King Aerys accused Brandon of plotting to murder the prince and had him and his companions, including Ser Elbert Arryn (the heir to the Vale), taken into custody. He ordered their fathers present themselves to explain their sons' behaviour. He had all of them killed, Brandon by strangling and Lord Rickard by immolation.
Eddard Stark, the second son of Lord Rickard, was visting his friend and mentor, Lord Jon Arryn, at the Eyrie at this time. Lord Robert Baratheon, the young lord of Storm's End and Eddard's best friend, was also present. More importantly, Robert was betrothed to marry Lyanna. When King Aerys sent a message demanding that Jon hand over Eddard and Robert to the crown, Jon raised the banners of the Vale in revolt rather than allow his former wards be killed. Jon and Eddard had both suffered the unjustified deaths of family members, including the Lord of the North, whilst Robert's betrothed had been kidnapped, apparently against her will. They agreed that this justified that action be taken against the king.
House Stark, House Arryn and House Baratheon all called their banners and began assembling armies. Jon and Eddard entered into negotiations with Lord Hoster Tully, whose daughter Catelyn had been betrothed to the murdered Brandon. After some discussions, Eddard married Catelyn in his brother's place whilst Jon married her sister, Lysa. House Tully then joined the war on the rebels' side, ordering a full call to arms. The call was answered by all the Tully bannermen with the exception of House Darry, who declared for Aerys, and House Frey, who did not declare for the either side until shortly after the Battle on the Trident, when the war was all but won . On top of that House Nocher led by the foreigner Alek Nocher a childhood friend of Robert also sided with the rebels.
Realising what was happening, King Aerys summoned his own banners. The houses sworn directly to House Targaryen responded, as did the forces of House Tyrell, which commanded the most populous region in the Seven Kingdoms and hence the largest army. However, whilst House Martell vocally pledged support, privately Prince Doran was furious at the insult to his sister's honour, and mustered his troops with extreme lethargy. Disturbingly, Tywin Lannister refused to answer Aerys' summons and did not muster his forces, although he also seemed unmoved by requests from the rebels to join them as well. As always, House Greyjoy chose not to get involved in the affairs of the mainlanders.
The rebels realised that they needed an undisputed leader to command their forces and to replace Aerys once he was removed. To his dismay, they chose Robert, as his grandmother had been the daughter of King Aegon V Targaryen, giving him the best claim to the throne outside of Aerys and his children and grandchildren. Thus, Robert Baratheon claimed the Iron Throne.
The southern front
Whilst on paper the rebels enjoyed a slight numerical superiority as long as Houses Greyjoy, Lannister and Martell chose to remain out of the fighting, their strength was divided, with the Baratheon armies mustering in the Stormlands many hundreds of miles from where the Stark, Arryn and Tully forces were gathering in the northern Riverlands. Robert managed to return home safely, but found gathering his forces in close proximity to the hostile Reach lords and those of the Crownlands problematic. The situation was not improved by some of the storm lords and river lords rejecting their liege lords' commands and instead declaring for the king.
However, Robert was a charasmatic leader, a strong warrior who led from the front and also skilled tactically. The Tyrell armies posed the greatest threat to the rebel cause, but due to the size of the Reach would take some time to assemble. He decided to go on the offensive, leaving his brother Stannis to hold Storm's End. Intelligence revealed that forces commanded by Lord Grandison, Cafferen and Fell were planning to attack his army after gathering near the ruins of Summerhall. Robert surprised them by attacking each army as it came upon the field, defeating it in turn and then waiting for the next to arrive. Winning three battles in one day added to Robert's reputation, and his charisma won the three lords and their men to his cause.
Robert advanced west to Ashford, but he had been outmaneurvered by Lord Randyll Tarly, the most experienced general under Lord Mace Tyrell. Tarly had assembled a strong force in record time and took this army's vanguard ahead of the main force. Despite being outnumbered by Robert's forces, he held them at bay long enough for the main Tyrell host to arrive. Desperately outnumbered, Robert was forced to withdraw from the field. Mace Tyrell took the credit for the victory, boasting how he had 'smashed' Robert's armies, but in reality Robert's forces remained more or less intact, and Tarly had done nearly all the fighting.
With the Tyrell armies now fully mobilised, Robert had no choice but to abandon the southern front and attempt to link up with his allies in the north. To this end he force-marched his troops north towards the Riverlands.
By this time, Aerys was furious with the lack of success in the war and replaced his Hand, Lord Owen Merryweather, with Ser Jon Connington. Connington was tasked with assembling an army out of the river lords who had remained loyal to the king, along with other forces from the Crownlands. Learning that Robert was marching north with his forces, Connington decided to intercept Robert and prevent his reunion with the northern armies. He succeeded in scattering Robert's forces (although most of them survived and managed to cross the Blackwater to link up with the other armies). Robert himself went to ground in the town of Battle of Stoney Sept and Connington was unable to flush him out before another force led by Eddard Stark arrived, compelling Connington to withdraw whilst locked in single combat with the rebel lieutenant Alek Nocher. For his failure Connington was stripped of his rank and exiled to the Free Cities, and was replaced by Lord Qarlton Chelsted as Hand of the King, whilst Ser Jonothor Darry of the Kingsguard took command of his army.
The northern front
Meanwhile, additional fighting had been taking place in the north. Eddard Stark had returned north by sea to see to the muster of the northmen, but his ship was shipwrecked on Sweetsister. Lord Borrell knew that his liege lord, Lord Sunderland, although an Arryn bannerman, harboured royalist sympathies and would want Eddard taken prisoner for a ransom. Lord Borrell chose to release Eddard instead, and he returned home safely.
Whilst the forces of the Vale were able to muster with no major problems, Lord Tully encountered difficulties. Several of his bannermen had sided with Aerys instead, leading to fighting across the Riverlands, whilst Lord Walder Frey, whilst proclaiming his allegiance, refused to commit his 4,000 troops to the war. In addition, the continued hesitation from Tywin Lannister left a potential threat to the Riverlands' flank should he choose to side with the king. As a result, the war in the north bogged down into a number of minor skirmishes and battles.
The arrival of the northmen changed things, and Eddard led a determined sally down the western shore of God's Eye to rescue Robert at Stony Sept. Upon his return, and with most of Robert's army including the sellswords hired for him by Alek Nocher now added to the rebel force, the rebels had enough strength to launch an assault on King's Landing. The bulk of the Tully and Arryn forces assembled on the north-eastern banks of the Green Fork and once joined by the Starks and Baratheons, they marched south along the Kingsroad to the main crossing point over the Trident.
By this time, Prince Rhaegar had reappeared to take command of the royalist army. Lord Aerys has made representations to Prince Doran Martell that his sister remained in King's Landing and in his power, whilst in a similar letter to Lord Tywin he commented that his son, Ser Jaime, as a member of the Kingsguard was in danger of being sent into the most threatening situations. Both threats seemed to work, and the Martells committed their forces to the cause, whilst, eventually, word came that Lord Tywin was leading an army to help defend the capital. Ser Lewyn Martell of the Kingsguard assumed command of the Dornish forces, and joined them to Rhaegar's royalist army at the Trident, although the Lannister host was still too distant to lend aid. Ser Jonothor Darry of the Kingsguard rallied the forces defeated at Stony Sept and joined them to Rhaegar's army as well.
The royalist army, outnumbering the rebels by several thousand troops but considerably less experienced, met the rebels in the Battle of the Trident. The battle was a bloody one fought over the river crossing, but Robert proved victorious. He killed Prince Rhaegar in single combat, whilst Ser Lewyn was slain and Ser Barristan Selmy of the Kingsguard was wounded and forced to yield. With their commanders killed or incapacitated, the royalist army routed, leaving the road to King's Landing open.
Robert had taken a wound, so Eddard Stark led the rebel army straight down the road towards the capital alongside Alek Nocher, racing to reach it before the Lannister reinforcements. He failed, as the Lannister army arrived at the city several hours before his own forces. However, Lord Tywin had no intention of helping to save King Aerys. His army brutally sacked the city and wiped out the defenders. Ser Jaime turned his cloak and slit Aerys' throat at the foot of the Iron Throne itself. Lannister bannermen stormed Maegor's Holdfast and killed Elia and her children, ending a potential rival threat to the throne.
Once that was done, Lord Tywin swore loyalty to Robert Baratheon and surrendered the city to Eddard Stark when he arrived, thus effectively ending the war, although some fighting continued in the south.
Eddard Stark disapproved strongly of the murder of Princess Elia, Prince Aegon and Princess Rhaenys, which caused a rift between him and Robert. Eddard left with another army to travel to Storm's End, where he accepted Lord Mace Tyrell's surrender and oath of loyalty to Robert.
Storm's End, remarkably, had not fallen despite being under siege for a year. Lord Stannis' garrison had been kept alive by entrepreneurial smugglers led by a freesail named Davos. For his services, Stannis raised him to knighthood, although he felt compelled by justice to remove the ends of Davos' fingers on one hand for his previous crimes.
Eddard learned that his sister was being held captive at a place called the Tower of Joy, a stone tower that Rhaegar had built for her in the shadow of the Red Mountains. He took six companions with him, to find the last three unaccounated-for members of the Kingsguard present: Lord Commander Gerold Hightower, Ser Arthur Dayne (the Sword of the Morning) and Ser Oswell Whent. Despite the numbers, Eddard's force was almost wiped out. Only he and Lord Howland Reed survived the skirmish alive, with Eddard himself slaying Arthur Dayne. Eddard was distraught to find his sister dying on a 'bed of blood', and was with her when she passed. He took the news of her death to Robert, and they were reconciled by their shared grief. Alek Nocher was made an official lord in the Vale as well as the Crownlands for his participation in the war and long running friendhsip with Robert. Eddard left to return Ser Arthur Dayne's sword, Dawn, to his sister at Starfall, whilst Robert agreed to marry Tywin's daughter, Cersei, in gratitude for his services in the war.
The remaining Targaryen loyalists had holed up on Dragonstone with the still-formidable Targaryen royal fleet, and Stannis Baratheon and Paxter Redwyne needed some time to assemble a fleet large enough to breach the defences. However, eight months after the Trident, the greatest storm seen in the Narrow Sea in living memory smashed the royal fleet to kindling on the rocks surrounding the island. Queen Rhaella died in childbirth that same night. Ser Willem Darry and some loyal soldiers took Prince Viserys and the newborn Princess Daenerys to safety in the Free Cities, whilst Dragonstone was captured by Stannis' forces.