This hypothesis was disproved when Shockwave discovered three female breaking into a Decepticon energon storage facility. Despite facing one of the Autobots' most formidable adversaries, the three female Autobots escaped unscathed; however, unbeknownst to three fugitives, Shockwave had dispatched a Sentinel to track them to the lair. The Sentinel was destroyed, but not before Shockwave approximated the rough location of the female Autobot headquarters.
At Shockwave's behest, Megatron sent a small squad of Decepticons led by Starscream to exterminate the female Autobots. The pounding pylons of Rumble trapped the female Autobots inside their own underground base. Alone and unaided, Elita-One engaged the Decepticons in a battle, the end result being the capture of Elita-One. With their new-found hostage, the Decepticons openly flaunted their victory and taunted the Earth-bound Autobots. Uncharacteristically emotional and irrational at this point, Prime left alone to free Elita-One, though he was followed by a team of his fellow Autobots.
Facing the Decepticons alone, Prime offered himself in exchange for Elita-One. All too eager to agree, the Decepticons accepted and placed him over a vat of acid powerful enough to destroy even a Transformer. In order to stop the execution, Elita-One utilized her damaging and highly draining special power--the stoppage of time. With whatever minimal strength she had remaining, Elita-One reanimated Prime from his time-frozen state and collapsed in his arms. Determined not to let her die, Prime drove off with Elita-One in his trailer in search of Alpha Trion. When the effects of Elita-One's power wore off, the Decepticons saw an old chassis melting in the acid and incorrectly assumed that it was Prime.
At this point, the other Autobots from Earth fought the Decepticons unsuccessfully with the now-freed female Autobots. As the battle raged on, Prime located Alpha Trion and bid him repair his love. Alpha Trion saw that she had used her experimental special power to save Prime's life and was forced to reveal the creator-creation relationship he shared with both Elita-One and Optimus Prime, who previously had not known whom was his creator.
The Autobot squadron on Cybertron, led by Ironhide, fared poorly against the Decepticons. Just before Shockwave was about to blow them off a steep ledge with a powerful blast in his gun mode, Optimus and the freshly-repaired Elita-One made a cavalry charge and turned the tide of the battle against the Decepticons, who wisely decided to flee against the might of the two Autobot leaders.
In the aftermath of the fight, Prime and Elita-One were forced to part once again, both being too important to their respective causes on Earth and Cybertron to stay away. The pair reluctantly acknowledged this and wished each other the best in their never-ending struggle against the evil Decepticon forces.