No they didn't just find the reckage, they also happened to completely miss the Autobots & Decepticons that were just there, and happen upon his ship during the kamikaze run in time to rescue the dead prime just in time, then got contaminated by evil red cosmic spores that were coming off of the star Prime was crashing into, or something like that. Or maybe this was the nexus episode between the pre- & post Beast Wars temperal screw up, and thats why they were able to save an intacct Optimus. Regardless, he looked badass with his eye socket exposed!
That's not the true failing of the 3rd season though. The real failing was whiny bitchass Rodimus Prime. At the end of the movie, he was all poised to take leadersihp, but then as of the first post moive ep, he was all emo & weak. Maybe it was because they were already considering bringing back Op after the movie backlash, but somewhere along the line both Rodimus & Galvatron got nuetered. Had we gotten our proper Flintimus Prime, and badass Nimoy version Galvatron, that could have been a far superior season.