Dear Vector Prime, In the Transformers × Evangelion universe, was the intervention of the Autobots enough to prevent the success of the Human Instrumentality Project (AKA Third Impact)? And did they ever meet Shinji (the pilot of Evangelion Unit-01)?
Dear Angelic Asker,
I do recall the universe you are referring to. Paradoxically, it came into existence as a result of proceedings within itself, when a powerful Anti-A.T. Field briefly broke down the veil separating the Multiverse from the wider Omniverse. I was able to perceive events there up to that point, but soon after the Field dissipated my awareness of it began to cloud. Nonetheless, I will relay to you what I saw.
Following the defeat of the Starscream-possessed Third Angel at the hands of Optimus Prime, the Autobots chose to establish a greater presence on Earth, working more closely with NERV to defend Tokyo-3. Research into Prime's mysterious upgraded form yielded fruit after the Fifth Angel caused immense thermal damage to Unit-00, prompting NERV to rebuild the Evangelion's superstructure using the knowledge gained. The upgraded Unit-00, now able to convert into a truck just like Optimus Prime, also gained impressive mass-shifting capabilities, allowing it to change the sizes of its individual body parts at a whim. These advancements were quickly replicated with Unit-01 and Unit-02, and proved most useful in the battles against the Angels.
Once the angels were defeated, SEELE sought to bring about Human Instrumentality—but with the Lance of Longinus stranded on the moon, there was only one medium remaining with which to begin Third Impact: the Autobot Matrix of Leadership. After a failed hacking attempt of the Teletraan/Magi networked intelligence, SEELE instead resorted to more duplicitous means, fabricating evidence that NERV was planning to begin Third Impact themselves, which they passed to the one government agency with the military strength to rival NERV's.
The sounds of gunfire and the berserker cry "G.I. Joe!" soon filled the GeoFront. Hundreds of NERV operatives, including noncombatants, were slaughtered by America's elite special mission force—but this would prove to be barely a drop in the ocean. Although the Autobots refused to counterattack against the humans, the Evangelions had no such compunctions, and were eventually able to wipe out G.I. Joe.
It all came tumbling down when SEELE revealed their final contingency: an alliance brokered with the Decepticons. Galvatron himself tore the Matrix from Prime's chest, thus beginning Third Impact. Every living soul on Earth was transmuted into pure Energon, and all became one.
I do not know of this "Shinji" of which you speak. The name of Evangelion Unit 01's pilot was Spike. In what little time they shared together, Optimus Prime became the father he never had, and I think that was what saved him.