In August of 3049, while hunting down a pirate band in the Periphery, near the border of the Free Rasalhague Republic, a company of the Kell Hounds mercenary unit was comprehensively defeated by an unknown enemy. Among the missing was Phelan Kell, son of Kell Hounds' commander Morgan and cousin of Victor Davion. He was initially presumed dead, but was in fact captured and adopted into Clan Wolf as a bondsman. He would later play a major role in the invasion and the future of the Wolf Clan.

The Kell Hounds' defeat on The Rock was just the first of many suffered by Inner Sphere forces, at the hands of the invading Clans, as the descendants of the SLDF troops, who departed the Inner Sphere with General Kerensky over 300 years ago, sought to restore the Star League in his name.

After a series of probing strikes, designed to test the mettle of their enemy, the Clans finally struck in force in March of 3050, attacking the Draconis Combine, the Free Rasalhague Republic and the Lyran half of the Federated Commonwealth. The speed and ruthlessness of their attacks, combined with their technological superiority saw them roll over their Inner Sphere opponents with ease, capturing large swathes of Combine and Commonwealth territory, as well as virtually the entire Rasalhague Republic.

The Clans' advance into the Inner Sphere was finally halted on October 31st 3050, when a Rasalhague pilot, named Tyra Miraborg, crashed her damaged Shilone fighter into the bridge of the Clan Wolf flagship, the Dire Wolf, killing ilKhan Leo Showers. The death of the Clans' war leader accomplished what 6 months of fighting had failed to. Putting all future assaults on hold, they garrisoned the worlds they had already conquered and returned to Clan space to elect a new ilKhan. In late 3051, Khan Ulric Kerensky of Clan Wolf was chosen to lead a renewed assault on the Inner Sphere.

During the lull in the fighting, Colonel Jaime Wolf, commander of the Wolf's Dragoons mercenary unit, called the heads of the Successor States to a meeting on their homeworld of Outreach. There, he revealed the Dragoons' origins - that they were actually Clan warriors - albeit freeborns, rather than the genetically "pure" trueborns. After managing to calm the furore that naturally erupted over this revelation, he further surprised his visitors by stating that the Dragoons were willing and able to help defend the Inner Sphere against their former kinsmen.

Even after placing their faith in Dragoons, there was still the matter of overcoming the centuries-old rivalries between each other. Progress was made when Hanse Davion and Theodore Kurita signed a non-aggression pact, securing a truce between the Federated Commonwealth and Draconis Combine. Additionally, Davion sought support from the Free Worlds League, in the form of arms and other supplies. In return he agreed to take Thomas Marik's cancer-stricken son Joshua to the New Avalon Institute of Science, where their considerable resources would be devoted to curing his leukaemia.

In November of 3051, the Clans resumed their invasion and by January of 3052, they were on the verge of conquering the Draconis Combine. Clans Smoke Jaguar and Nova Cat struck the Combine capital of Luthien. Risking criticism and loss of support from his own people, Davion sent the Dragoons, together with the Kell Hounds to aid the Combine forces. This helped cement the alliance with his old adversary and allowed both nations to focus all their efforts on fighting the Clans. With all eyes firmly focused on the Clans, no-one could have foreseen the threat developing in their midst.

Shortly after the invasion, Comstar opened negotiations with the Clans, who accepted their offer to administrate the worlds they conquered. Comstar's then-leader, Primus Myndo Waterly, planned to use the invasion to engineer the collapse of civilisation in the Inner Sphere, allowing Comstar to step up as the saviour of mankind, gaining control over the Successor States in the process.

Primus Waterly was forced to change her plans, when she learned the Clans intended to conquer Terra. Following some hurried negotiations, Comstar agreed to fight the Clans in a bid to halt the invasion. The battle, between the massed Com Guard forces and units representing all the invading Clans, took place on the world of Tukayyid in the Free Rasalhague Republic, in May 3052. It remains the largest pitched battle ever fought in Inner Sphere history. The battle lasted for 2 weeks and although losses were heavy on both sides, the Com Guards emerged victorious, forcing the Clans to halt their conquest of the Inner Sphere for 15 years. The Truce of Tukayyid, as it was know, was accepted with good grace by the Warden Clans, but bitterly resented by the Crusaders, particularly those units who had not particpated in the battle and therefore felt they should not be bound by the agreement.

However, Waterly wasn't about to give up on her plans for domination of the Inner Sphere. While the Battle of Tukayyid was underway, she gave word to agents in ROM (Comstar's intelligence service) to launch a series of guerilla attacks, on worlds in the various Clan Occupation Zones, as well as the HPG networks of the Successor States, codenamed Operation Scorpion. By doing this, she hoped to cripple the Clans' ability to control the worlds they had conquered and the Successor States' ability to control their military forces.

In the resulting chaos and confusion, Comstar, or at least the faction loyal to Waterly, would seize control of all interstellar communications, effectively gaining control of the Inner Sphere. As it turned out, many of these planned strikes failed. When Precentor Martial Anastasius Focht learned of Operation Scorpion, following the Com Guards' victory on Tukayyid, he returned to Terra and deposed Primus Waterly. He then set about reforming Comstar, to make it a less secretive organisation and curtail its covert activities.