In the year 390 AC, Houses Hightower, Martell, Tully, and Velaryon led a rebellion against the long-reigning King Baelon I Blackfyre, to place Matarys Targaryen, an alleged descendent of the heroes Jon Snow and Danerys Targaryen, on the Iron Throne.
The Targaryens Emerge
In 388 AC, at a tourney at Highgarden later known as the Tourney of the Golden Roses, Lord Hightower began to gain support for his new good-brother, Matarys 'Targaryen', having recently wed his younger sister, Rhaelle.
Matarys and his family gained the assistance of House Hightower, a once loyal vassal of the red dragons, in their attempt to seize the Iron Throne. Prior to being sheltered at the Hightower in Oldtown, the Targaryens spent the past century in various places, including the dragon-invested island of Dragonstone. While on Dragonstone, the Targaryens were assisted by the Velaryons to remain hidden.
Although the new "Targaryens" resemble the blood of Old Valyria and once resided in the ancestral seat of the ancient house, they had no actual proof of their claim to be Daenerys' kin. Similar to the Blackfyres, none of the Targaryens had successfully tamed a dragon since Daererys herself.
The realm split into factions following Matarys' reveal; either supporting the rebels, led by House Hightower, or the loyalist to the Iron Throne. Some houses even choose to stay neutral such as Houses Connington, Baratheon, and Stark.
Lines are Drawn
Lord Hightower was the first supporter of the Targaryen claimant, Matarys, being promised the Lord Paramountcy in return. Lord Paramount Lorent Tyrell branded Hightower a traitor to the realm after declaring war on the the Blackfyres, raising his own banners in favor of King Baelon I Blackfyre.
In the Riverlands and Dorne, both Houses Martell and Tully choose to join House Hightower in supporting the Targaryens; these were Matarys Targaryen's strongest supporters militarily.
Prince Aeron Martell of Dorne sent his son and heir, Calon Martell, to lead the Dornish forces early in the war. However, the bulk of House Martell's armies were not able to join the fighting north of the Red Mountains because House Yronwood, a long-standing Blackfyre supporter and rival of House Martel, called their own banners in name of King Baelon, despite their Prince's call to arms. Although Yronwood successfully blockaded the use of the Stoneway and thus nearly half of Prince Aeron's forces, Houses Dayne, Blackmont and many others were able to join the fighting in the Reach with the use of the Prince's Pass.
Despite House Tully being a former loyalist of the Blackfyres following their reinstatement to the Lord Paramountcy at the end of the War of the Five Kings, they chose to support Matarys over King Baelon. Lord Alyx Mallister of Seagard, good-brother to Riverrun's Lord Symond Tully, defied the Tullys and supported the Blackfyres with the assistance of several other river lords.
Dragon vs Dragon
Battle of the Tumblestone
One of the first full scale battles of the conflict was when the Lannisters attacked the Tully army along the Tumblestone. Approximately 25,000 Lannister troops, under the command of Lord Tyrek Lannister, met Ser Symond Tully's host.
At around noon the Lannister troops crossed the ford a few miles northwest of Riverrun. Tully forces soon engaged the Lannister host. The Lannister army formed a shield wall while their outriders harassed the advancing Tully army to give them time to get prepared for a battle. Behind the Lannister shield wall was a line of archers, ready to fire at Tully troops.
The first engagement was the Tully cavalry charge to attempt to break the Lannister lines. Around 1,000 mailed Tully knights charged the green Lannister levies. Lord Tyrek ordered a premature volley in an attempt to intimidate the knights into retreating but to no avail. Lord Tyrek then sent 2,000 Lannister knights to intercept the Tully knights before they reached the shield wall. The countercharge worked and sent the Tully knights into a full retreat while the Lannisters suffered minor losses.
The Tully infantry began to advance, walking until the archers could reach them, and them charging. Lord Tyrek commanded another volley, this time hitting its mark. As soon as the volley was fired the Tully infantry charged the shield wall, supported by archer fire. The Tully forces began to make holes in the shield wall, spilling out behind them.
The right flank, lead by Lord Tyrek’s son Ser Gerion Lannister was heavily embroiled in fighting. Lord Tyrek, seeing the wall crumble, tasked his brother, Ser Tommen Lannister, to lead the rest of the knights around the flank and smash into the Tully army’s side. Tommen did exactly that, and caused the Tully army to retreat as knights and spearmen cut them down. During the chaos, Lord Tyrek was struck by an arrow in his shoulder, throwing him from his horse and severely wounding him.
While the battle was an overall victory for the Lannisters and Blackfyre loyalists, they suffered many losses. The Tullys lost the vast majority of their own host, however, crippling them for the remainder of the war.
The Battle on the River Road
A relatively small, yet bloody, skirmish between loyalist and rebel forces near the Inn of the Kneeling Man, along the Red Fork and east of Riverrun. Lord Alyx Mallister was in command of the loyalist and ensured their victory. Following the battle, many of the loyalists celebrated the victory at the Inn of the Kneeling Man.
Stormlands Civil War
The Buildup
Lyonel Baratheon, Lord of Storm's End, had long desired to see the title of Lord Paramount returned to House Baratheon. At the time of the Targaryen Rebellion, however, it remained firmly in the hands of Lord Raymund Connington. When word of Matarys' host raising in Oldtown reached Storm's End, Lyonel made his move.
Using the connections he'd made with several Stormlords through marriage agreements with his many daughters, Lyonel called up a sizeable force of men to march on Griffin's Roost. Among these was House Seaworth, the house which his second wife had been born into.
The Siege of Griffin's Roost
Lyonel's host arrived at Griffin's Roost during the height of the Targaryen Rebellion, and it was for this that King Baelon was unable to respond to letters seeking his support as House Connington's oldest ally. After several weeks of fruitless siege, and at the urging of his younger brother Ser Borros Baratheon, Lyonel decided to storm the castle.
Atop the walls Lyonel and his men won a quick victory, breaking through into the keep itself, however he met Raymund Connington in single combat. Despite wounding the Lord of Griffin's Roost severely, Lyonel was killed in the duel.
Ser Borros, seeing his brother fall, flooded the castle with Baratheon men, and despite losing his brother, takes the castle. Raymund's family and household were taken captive, and when met with the ultimatum of petitioning the King to transfer the title of Lord Paramount to Domeric Baratheon, Lyonel's heir, or the imprisonment of his family, Raymund chose to surrender and gave in to Borros' demands. Within a fortnight a response came from the Iron Throne granting the title to House Baratheon.
Aftermath
The transfer of power was not the only result of the brief conflict. Borros Baratheon demanded that House Connington give a child to House Baratheon as a ward in an effort to keep the peace between the houses going forward. Going against his nature, Borros chose what he saw as a more merciful approach, and took Raymund's second son Criston as the ward instead of his heir Arlan. A contract was drafted stating that visits to him at Storm's End would be allowed, however Criston would stay at Storm's End until his eight-and-tenth nameday.
When everything was solidified, Criston was taken back to Storm's End to live out his time as a ward of House Baratheon. His twin sister, Ravella, needed to be restrained by her father's men when her protests against her brother's removal became violent.
The Conclusion
The war which became known as the Targaryen Rebellion ended later the same year it began, when Matarys Targaryen died in the field of battle alongside his brother Viserys, who was slain in personal combat with Desmond Clegane. The remaining Targaryens fled and scattered following the death of their patriarch.
The rebel houses bent the knee once more to King Baelon I Blackfyre, following the loyalist victory. Many sent their younger children as wards and hostages to the Red Keep, while others Targaryen supporters fled Westeros entirely. A relatively new sellsword company, the Sunset Swords, saw their numbers swell as exiles from Westeros joined their ranks.