In 2013, Bumblebee began an uneasy friendship with the Decepticon Jetfire. Jetfire managed to convince Bumblebee not to mount a large scale attack on the Decepticon space bridge. Instead, Bumblebee agreed to keep a low profile while Jetfire acted as a double agent. The plan did not come without sacrifice, however. To ensure Jetfire a high place in the Decepticon hierarchy, Bumblebee allowed Jetfire to "discover" their main underground headquarters. In addition, Bumblebee allowed Ultra Magnus to sacrifice himself in a fight with Jetfire.
After the Decepticons overtook the Autobots' main base and the death of Ultra Magnus, Springer issued a direct challenge to Bumblebee's leadership, imploring the gathered Autobots vote "no confidence" in Bumblebee's leadership and install Springer as interim leader. He vowed to begin using Decepticon tactics and begin a campaign to instill terror in the Decepticons' psyche by conducting small, but deadly raids. While he had the support of the senior Autobot leader Hot Spot, Springer's initiative ultimately failed (263 voted "No Confidence", 327 voted against). Despite losing, Springer vowed to support Bumblebee and ordered all of his followers to follow his lead. In a gesture of solidarity, Bumblebee promoted Springer to City Commander, the position held by the deceased Ultra Magnus.
Bumblebee, with the help of Sky Lynx, Grimlock, Jetfire, and Springer, rallied the Autobots for a daring raid on the Decepticon Space Bridge. On the third and final transport of Autobots to their new home of Nebulous, Shockwave blasted the Space Bridge, almost destroying it, and instantly killing almost 40 elite Autobot warriors, leaders, and scientists. However, the Space Bridge remained intact and Bumblebee and the rest of the Autobots were able to escape to Nebulos. While on Nebulos, Typhoon presented Bumblebee the Autobot Matrix of Leadership, which was recovered from Megatron. Typhoon and Perceptor presented the Matrix of Leadership to Bumblebee. He accepted and was awarded the title of Prime.
- 2013 October - "A Chance Encounter" - A young Decepticon scientist travels to Cybertron, shaken by what he has seen on Earth. He hopes to find peace on the metal world, but a chance encounter with a small Autobot leads to his entire world view being altered.
- October, 2013 - "The Second Meeting" - Bumblebee and Jetfire meet again. The young Decepticon asks to learn more of Optimus Prime, and gives Bumblebee an idea on how to save the remaining Autobots.
- October, 2013 - "The Gift of Trust" - Jetfire and Bumblebee meet for the third time, and Jetfire asks Bumblebee for something he can give to Megatron to curry favor with the Decepticon Leader.
- October, 2013 - "A Hero's Sacrifice" -
Jetfire is brought to a meeting with the leaders of the Autobots. There he outlines the plan he and Bumblebee have come up with. Gradually, the group comes to a sobering realization: someone must die to ensure the future of the Autobots.
- 2013 November - "A Final Run Through" - Bumblebee, Jetfire, and a skeptical Springer meet to go over the final plans of a daring raid that will do nothing less but provide either a fighting chance against their Decepticon oppressors, or give the remaining Autobots a permanent resting place.
- 2013 - November - "Escape to Nebulos" - Bumblebee and Springer lead all the Autobots to the Space Bridge for a last-ditch effort to escape certain death under Decepticon-controlled Cybertron.