When the Livonian Brothers of the Sword launched their crusade in 1208, the pagan Estonians had been raiding south into recently Christianized territory for years. Denmark joined the crusade in 1219. Sweden tried in 1220 and was destroyed by Estonian counterattack. By the winter of 1220, however, almost all of continental Estonia had fallen to the Germans and Danes, and the population had been declared Christian. The peace lasted three years. In 1223 the Estonians rose in a coordinated revolt across the mainland: Germans and Danes who fell into their hands were killed, some of the priests sacrificed to the old gods, the captured fortresses re-garrisoned. The leaders of Ugaunia and Sakala knew they could not hold against the crusader counterattack alone. They sent to Novgorod and Pskov for mercenaries. Two hundred Russian fighters arrived in Tartu under Vyachko, a prince who in 1208 had lost his own seat at Koknese to the same Sword Brethren who were now coming for him.

The Germans took back the smaller fortresses through the winter of 1223-1224, one after another. By Easter 1224, only Tartu remained a center of Estonian resistance in southern Estonia. Diehard fighters had gathered there from Sakala and other nearby provinces; the fortress on Toomemagi, the Cathedral Hill above the Emajogi River, was packed with families. The first crusader siege after Easter lasted only five days before the besiegers withdrew. The bishops sent envoys offering Vyachko safe passage if he would surrender the Estonian rebels. Vyachko refused. The Novgorodian princes, the chronicle says, had promised him the fortress and the surrounding lands as his own dominion if he could conquer them, and he intended to keep that promise. He told the envoys to go away and waited for the army from Novgorod that he believed was coming.

On 15 August 1224, the crusader army returned, reinforced this time with large numbers of Christian Latvian and Livonian troops fighting alongside the Germans. The siege lasted many days and nights. The crusaders built bricoles, the small stone-throwing engines that could lob hot iron and fire-pots over the walls, and rolled a high siege turret slowly toward the ramparts. They mined under the walls and gathered wood to set the timber on fire. The defenders fired their own bricoles and crossbows. At night, the Chronicle of Henry says, the fighting continued in noise as well as steel: men shouting at each other across the dark, drumming, blowing horns, ringing their swords on shields. When the final assault came, the wall was breached and the fighters poured in. Every defender of Tarbatu died: the Estonian men, the women who fought beside them, Vyachko's Russians who tried a last stand in one of the fortifications and were dragged out. Henry of Livonia put the Estonian dead at nearly a thousand. The single Russian survivor was sent away on his horse to tell Novgorod what had happened.

With Tartu fell the last continental Estonian polity. Only the islands, Saaremaa and Hiiumaa, would hold their independence for a few years more before they too were taken. Russia lost its last foothold in Estonia. The Pope's legate, Wilhelm of Modena, arrived later that year and established the Bishopric of Tartu in the conquered land. A medieval Catholic city grew up beneath Toomemagi, with a German bishop, German merchants, and Estonian peasants in the hinterland; the cathedral on the hill was begun in the thirteenth century and stood for three hundred years before the Reformation took its roof. Today Toomemagi is a leafy hill in the center of Tartu, Estonia's second city, and the ruins of the cathedral stand at its summit. The University of Tartu, founded in 1632 by King Gustavus Adolphus of Sweden, occupies the buildings around the hill. The plaque most visitors read on Cathedral Hill is about the university; the older history, the night fighting and the burning timber and the one survivor with his horse, is a layer down.