Agnes assigned the Duchy of Bavaria, given by her husband to Henry IV, to Otto of Nordheim. This deprived the young king of a solid base of power. Likewise, her decision to assign the Duchies of Swabia and Carinthia to Rudolf of Rheinfelden (who married her daughter Matilda) and Berthold of Zähringen, respectively, would prove mistakes, as both later rebelled against the king. Unlike Henry III, Agnes proved incapable of influencing the election of the new popes, Stephen IX and Nicholas II. The Papal alliance with the Normans of southern Italy, formed to counter the communal resistance in Rome, resulted in the deterioration of relations with the German King, as well as Nicholas' interference in the election of German bishops. Agnes also granted local magnates extensive territorial privileges that eroded the King's material power.
In 1062 the young king was kidnapped during a conspiracy of German nobles led by archbishop Anno II of Cologne. Henry, who was at Kaiserwerth, was persuaded to board a boat lying in the Rhine; it was immediately unmoored and the king sprang into the stream, but was rescued by one of the conspirators and carried to Cologne. Agnes retired to a convent, the government subsequently placed in the hands of Anno. His first move was to recognize Pope Alexander II in his conflict with the antipope Honorius II, who had been initially recognized by Agnes but was subsequently left without support.
Anno's rule proved unpopular. The education and training of Henry were supervised by Anno, who was called his magister, while Adalbert of Hamburg, archbishop of Bremen, was styled Henry's patronus. Henry's education seems to have been neglected, and his willful and headstrong nature developed under the conditions of these early years. The malleable Adalbert of Hamburg soon became the confidant of the ruthless Henry. Eventually, during an absence of Anno from Germany, Henry managed to obtain the control of his civil duties, leaving Anno only with the ecclesiastical ones.
In 1066, one year after his enthroning at the age of fifteen, he expelled Adalbert of Hamburg, who had profited off his position for personal enrichment, from the Crown Council. Henry also adopted urgent military measures against the Slav pagans, who had recently invaded Germany and besieged Hamburg.
In June 1066 Henry married Bertha of Maurienne, daughter of Count Otto of Savoy, to whom he had been betrothed in 1055. In the same year he assembled an army to fight, at the request of the Pope, the Italo-Normans of southern Italy. Henry's troops had reached Augsburg when he received news that Godfrey of Tuscany, husband of the powerful Matilda of Canossa, marchioness of Tuscany, had already attacked the Normans. Therefore the expedition was halted.
In 1068, driven by his impetuous character and his infidelities, Henry attempted to divorce Bertha. His peroration at a council in Mainz was however rejected by the Papal legate Pier Damiani, who hinted that any further insistence towards divorce would lead the new pope, Alexander II, to deny his coronation. Henry obeyed and his wife returned to Court, but he was convinced that the Papal opposition aimed only at overthrowing lay power within the Empire, in favour of an ecclesiastical hierarchy.
In the late 1060s Henry set up with strong determination to reduce any opposition and to enlarge the national boundaries. He led expeditions against the Liutici and the margrave of a district east of Saxony; and soon afterwards he had to quench the rebellions with Rudolf of Swabia and Berthold of Carinthia. Much more serious was Henry's struggle with Otto of Nordheim, duke of Bavaria. This prince, who occupied an influential position in Germany and was one of the protagonists of Henry's early kidnapping, was accused in 1070 by a certain Egino of being privy to a plot to murder the king. It was decided that a trial by battle should take place at Goslar, but when the demand of Otto for a safe conduct for himself and his followers, to and from the place of meeting, was refused, he declined to appear. He was thereupon declared deposed in Bavaria, and his Saxon estates were plundered. He obtained sufficient support, however, to carry on a struggle with the king in Saxony and Thuringia until 1071, when he submitted at Halberstadt. Henry aroused the hostility of the Thuringians by supporting Siegfried, archbishop of Mainz, in his efforts to exact tithes from them; but still more formidable was the enmity of the Saxons, who had several causes of complaint against the king. He was the son of one enemy, Henry III, and the friend of another, Adalbert of Bremen. He had ordered a restoration of all crown lands in Saxony and had built forts among this people, while the country was ravaged to supply the needs of his courtiers, and its duke Magnus was a prisoner in his hands. All classes were united against him, and when the struggle broke out in 1073 the Thuringians joined the Saxons. The war, which lasted with slight intermissions until 1088, exercised a most potent influence upon Henry's fortunes elsewhere.
The tension between Empire and Church culminated in the councils of 1074–1075, which constituted a substantial attempt to delegitimate Henry III's policy. Among other measures, they denied to secular rulers the right to place members of the clergy in office; this had dramatic effects in Germany, where bishops were often powerful feudatories who, in this way, were able to free themselves from imperial authority. Aside from the reacquisition of all lost privileges by the ecclesiasticals, the council's decision deprived the imperial crown of rights to almost half its lands, with grievous consequences for national unity, especially in peripheral areas like the Kingdom of Italy.
Suddenly hostile to Gregory, Henry did not relent from his positions: after his defeat of Otto of Nordheim, he continued to interfere in Italian and German episcopal life, naming bishops at his will and declaring papal provisions illegitimate. In 1075 Gregory excommunicated some members of the Imperial Court, and threatened to do the same with Henry himself. Further, in a synod held in February of that year, Gregory clearly established the supreme power of the Catholic Church, with the Empire subjected to it. Henry replied with a counter-synod of his own.
The beginning of the conflict known as the Investiture Controversy can be assigned to Christmas night of 1075: Gregory was kidnapped and imprisoned by Cencio I Frangipane, a Roman noble, while officiating at Santa Maria Maggiore in Rome. Later freed by Roman people, Gregory accused Henry of having been behind the attempt. In the same year, the emperor had defeated a rebellion of Saxons in the First Battle of Langensalza, and was therefore free to accept the challenge.
At Worms, on January 24 1076, a synod of bishops and princes summoned by Henry declared Gregory VII deposed. Hildebrand replied by excommunicating the emperor and all the bishops named by him on February 22, 1076. In October of that year a diet of the German princes in Tribur attempted to find a settlement for the conflict, conceding Henry a year to repent from his actions, before the ratification of the excommunication that the pope was to sign in Swabia some months later. Henry did not repent, and, counting on the hostility showed by the Lombard clergy against Gregory, decided to move to Italy. He spent Christmas of that year in Besançon and, together with his wife and his son, he crossed the Alps with help of the Bishop of Turin and reached Pavia.
Henry's intent, however, was apparently to perform the penance required to lift his excommunication and ensure his continued rule. The choice of an Italian location for the act of repentance, instead of Augsburg, was not accidental: it aimed to consolidate the Imperial power in an area partly hostile to the Pope; to lead in person the prosecution of events; and to oppose the pact signed by German feudataries and the Pope in Tribur with the strong German party that had deposed Gregory at Worms, through the concrete presence of his army.
He stood in the snow outside the gates of the castle of Canossa for three days, from January 25 to January 27, 1077, begging the pope to rescind the sentence (popularly portrayed as without shoes, taking no food or shelter, and wearing a hairshirt - see Walk of Canossa). The Pope lifted the excommunication, imposing a vow to comply with certain conditions, which Henry soon violated.
Despite these difficulties, Henry's situation in Germany improved in the following years. When Rudolf was crowned at Mainz in May 1077 by one of the plotters, Siegfried I, Archbishop of Mainz, the population revolted and forced him, the archbishop, and other nobles to flee to Saxony. Positioned there, Rudolf was geographically and then militarily deprived of his territories (later he was also stripped of Swabia) by Henry. After the inconclusive battle of Mellrichstadt (August 7 1077) and the defeat of Henry's forces in the Flarchheim (27 January 1080) Gregory flip-flopped to support the revolt and launched a second anathema (excommunication) against Henry in March 1080, thereby supporting the antiking Rudolph. However, the ample evidence that Gregory's actions were rooted in hate for the Emperor-elect instead of theology had an unfavorable personal impact on the Pope's reputation and authority leading much of Germany to re-embrace Henry's cause.
On October 14 1080 the armies of the two rival kings met at the Weisse Elster River in the battle of Elster, in the plain of Leipzig and Henry's forces again suffered a military defeat, but won the battle with a strategic outcome— the anti-king Rudolf of Rheinfelden was mortally wounded and died the next day at nearby Merseburg, and the rebellion against Henry lost much of its momentum.
Soon after, another antiking, Hermann of Salm, arose as figurehead in the Great Saxon Revolt cause, but was fought successfully by Frederick I, Duke of Swabia (Frederick of Swabia)— Rudolf's Henry-appointed successor in Swabia who had married Henry's daughter Agnes of Germany. Henry convoked a synod of the highest German clergy in Bamberg and Brixen (June, 1080). Here Henry had pope Gregory (he'd dubbed "The False Monk") again deposed and replaced by the primate of Ravenna, Guibert (now known as the antipope Clement III, though who was in the right was unclear in the day).
Feeling secure of his success in Italy, Henry returned to Germany.
The Emperor spent 1084 in a show of power in Germany, where the reforming instances had still ground due to the predication of Otto of Ostia, advancing up to Magdeburg in Saxony. He also declared the Peace of God in all the Imperial territories to quench any sedition. On March 8 1088 Otto of Ostia was elected pope as Victor III: with the Norman support, he excommunicated Henry and Clement III, who was defined "a beast sprung out from the earth to wage war against the Saints of God". He also formed a large coalition against the Holy Roman Empire, including, aside from the Normans, the Rus of Kiev, the Lombard communes of Milan, Cremona, Lodi and Piacenza and Matilda of Canossa, who had remarried to Welf II of Bavaria, therefore creating a concentration of power too formidable to be neglected by the emperor.
Henry then launched his third punitive expedition in Italy. After some initial success against the lands of Canossa, his defeat in 1092 caused the rebellion of the Lombard communes. The insurrection extended when Matilda managed to turn against him his elder son, Conrad, who was crowned King of Italy at Monza in 1093. The Emperor therefore found himself cut off from Germany. He could return there only in 1097: in Germany his power was still at its height. Matilda of Tuscany had secretly transferred her property to the Church in 1089, before her marriage to Welf II of Bavaria (1072-1120). In 1095, a furious Welf left her and, together with his father, switched his allegiance to Heinrich IV, possibly in exchange for a promise of succeeding his father as duke of Bavaria. Henry reacted by deposing Conrad at the diet of Mainz in April 1098, and designating his younger son Henry (future Henry V) as successor, under the oath sworn that he would never follow his brother's example.
The situation in the Empire remained chaotic, worsened by the further excommunication against Henry launched by the new pope Paschal II, a follower of Gregory VII's reformation ideals elected in the August of 1099. But this time the emperor, meeting with some success in his efforts to restore order, could afford to ignore the papal ban. A successful campaign in Flanders was followed in 1103 by a diet at Mainz, where serious efforts were made to restore peace, and Henry IV himself promised to go on crusade. But this plan was shattered by the revolt of his son Henry in 1104, who, encouraged by the adherents of the pope, declared he owed no allegiance to an excommunicated father. Saxony and Thuringia were soon in arms, the bishops held mainly to the younger Henry, while the emperor was supported by the towns. A desultory warfare was unfavourable, however, to the emperor, who was taken as prisoner at an alleged reconciliation meeting at Koblenz. At a diet held in Mainz in December, Henry IV was forced to resign to his crown, being subsequently imprisoned in the castle of Böckelheim. Here he was also obliged that he had unjustly persecuted Gregory VII and to have illegally named Clement III.
When these conditions became known in Germany, a vivid movement of dissension spread. In 1106 the loyal party set up a large army to fight Henry V and Paschal. Henry IV managed to escape to Cologne from his jail, finding a considerable support in the lower Rhineland. He also entered into negotiations with England, France and Denmark.
Henry was also able to defeat his son's army near Visé, in Lorraine, on March 2 1106. He however died soon afterwards after nine days of illness, while he was guest of his friend Othbert, Bishop of Liège. He was 56.
His body was buried by the bishop of Liege with suitable ceremony, but by command of the papal legate it was unearthed, taken to Speyer and placed in the at that time unconsecrated chapel of Saint Afra that was build on the side of the Imperial Cathedral. After being released from the sentence of excommunication, the remains were buried in the Speyer cathedral in August 1111.
In 1089 Henry married Eupraxia of Kiev, a daughter of Vsevolod I, Prince of Kiev, and sister to his son Vladimir II Monomakh, prince of Kievan Rus. She assumed the name "Adelaide" upon her coronation. In 1094 she joined the rebellion against Henry, accusing him of holding her prisoner, forcing her to participate in orgies, and attempting a black mass on her naked body.
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