Before the war, a number of Cybertronians opposed the reign of Megatron and Optimus Prime. Four of these so-called Malcontents were holed up in Tyger Pax, where they were hunted down and murdered by the Defense Force. Megatron used the incident to convince Optimus to give him full leadership over Cybertron, so that he could do what was needed to protect its population. Optimus Prime obliged, and not much later, the Defense Force reformed itself into a faction, the Decepticons, and declared war on the Autobots of the Science Division. On Chromia's advice, the Autobots decided to leave their makeshift base at Burthov and set up a better, permanent one in Tyger Pax.

As the war dragged on, Sentinel Prime came up with a plan to stop the Decepticons, which required the Autobots to get a "torch" to the AllSpark in the Simfur Temple for it to become charged with the cube's energy. This was a problematic mission, as Simfur was in Decepticon hands, and thus a good strategy had to be prepared. With most of the Autobots keeping the Decepticons busy, Elita-One got the torch filled with energy and subsequently made a run for it to a place the Autobots had prepared two ships. Sentinel Prime instructed Wheeljack to take one of them and get the rest of the Autobots at Tyger Pax. Sentinel Prime's death shortly after made this unnecessary and Optimus Prime ordered the Autobots at Simfur to retreat and regroup at Tyger Pax.

With Sentinel Prime gone, Optimus Prime became sole leader of the Autobots. His first act was to take the AllSpark out of Decepticon hands.
300px-Foundation 3 Tyger Pax Nemesis