The secret siege occurred in 135 AC during the regency of Aegon III. When King Aegon III Targaryen and his brother, Prince Viserys, defiantly remained in Maegor's Holdfast within the Red Keep for eighteen days in order to protect Viserys' wife Larra Rogare from being arrested on the orders of the regents.
It became known as the "secret siege" due to the fact that the majority of both the population of King's Landing and the rest of Westeros was unaware of the siege until after its conclusion.
During the Lysene Spring, Prince Viserys Targaryen's wife, Lady Larra of Lys, and her family from House Rogare were accused of being part of a plot to overthrow King Aegon. Lord Thaddeus Rowan, the Hand of the King, was also implicated in the conspiracy and was arrested and taken to the dungeons where the Lord Confessor, Lord George Graceford began torturing him. Ser Marston Waters, the Lord Commander of the Kingsguard was appointed the new Hand by the council of regents and he ordered the arrest of Larra and her kin.
Ser Amaury Peake of the Kingsguard along with a dozen men-at-arms went to Maegor's Holdfast to arrest her, but Prince Viserys and King Aegon refused to give her up. Viserys planted an axe upon the drawbridge and warned Peake and his men not to cross it, before retreating back into the castle. When Amaury's men passed the axe, Sandoq the Shadow emerged and slew all the guards and Ser Amaury himself. After Sandoq was done, he retreated within the holdfast and the king commanded the portcullis be lowered and the drawbridge raised. King Aegon, Prince Viserys, Queen Daenaera, Lady Larra Rogare, Mushroom, several ladies in waiting, a few guardsmen and Sandoq would remain within the castle within a castle for eighteen days. Ser Raynard Ruskyn of the Kingsguard was within the holdfast too, but had been overwhelmed by Larra's Lysene guards and made a prisoner.
Though King Aegon and Prince Viserys had very few men within the holdfast, Ser Marston refused to storm the keep, as he did not wish to dishonor the white cloak by ordering an attack on the king he had sworn to protect. So it was decided to try and persuade the king and prince to leave with words. Ser Marston Waters, Ser Lucas Leygood the Commander of the City Watch, Grand Master Munkun, Septon Bernard, even the despised master-at-arms, Ser Gareth Long all tried to persuade the king to end the siege, but to no avail.
On the twelfth day of the siege, Lord Thaddeus Rowan was brought before the holdfast. After days of torture, Lord Thaddeus falsely confessed to being part of the plot with House Rogare to kill King Aegon and place Prince Viserys on the Iron Throne. The confession unraveled though when Viserys began asking him questions that Lord Rowan, weakened from the torture he experienced answered straight away in a meek and passive tone. Mushroom joined in and asked Lord Thaddeus if he had poisoned King Viserys I Targaryen and Lord Rowan acquiesced. Viserys and Aegon saw that Thaddeus had been broken, and had said what his torturers wanted to hear to stop the pain, making his confession invalid. King Aegon pointed this out to Ser Marston and ordered him to arrest those responsible for Lord Rowan's torture.
After the false confession of Lord Rowan, Marston recalled his duty and fulfilled his king's command to arrest those who had falsely implicated Thaddeus and the Rogares. Lord George Graceford was seized by the Kingsguard and soon implicated a dozen of men involved in a conspiracy to kill the Rogare family. Amongst the names was Ser Amaury Peake, Ser Mervyn Flowers, Tessario the Tiger, Septon Bernard, Ser Gareth Long, Ser Victor Risley, Ser Lucas Leygood and six of the seven captains of the city gates. Ser Marston was stabbed while trying to apprehend his own sworn brother, Ser Mervyn Flowers. Mervyn was subsequently beaten to death at the stables while trying to steal a horse. Ser Lucas was killed in a savage fight at the Gate of the Gods, three of the accused captains fled along with a dozen of their men. Tessario was taken captive near the River Gate, and later died under interrogation. The others were apprehended to face the king's judgment.
Even as all this was going on, King Aegon and Prince Viserys who were more mistrustful than ever, did not leave the safety of Maegor's Holdfast for another six days and that was only after they saw Grand Maester Munkun follow King Aegon's orders and dispatch a flock of ravens to several of Aegon's leal lords. By the time the king and his companions emerged from the holdfast, they had run out of food several days ago and were weak and exhausted from hunger.