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"End of the Line" and "Seeds of the Future: Part 3" both involved an Optimus-Megatron head to head. I THINK the episode you're talking about must be "End of the Line", since "Seeds of the Future" was the final Season 2 episode and had a very clear, definite finale. 1999 was also the year that Season One aired rather than Season 2. "End of the Line" was where Optimus went full fanatic and tried to turn Cybertron completely organic, only to regain his senses at the start of Season 2.
On the other hand, there were quite a few Beast Wars episodes that involved Optimus doing the Heroic Sacrifice thing (it was a bit of a habit for him), so if that still doesn't fit the bill, could you be thinking of the prequel series?
Edited by FantiSci
Can somebody tell me if this happened and what episode it was in? I specifically remember an episode of Beast Machines airing on Christmas Day 1999 but according to Wikipedia that did not happen, but I definitely remembering seeing an episode on that day, but I also can't find an episode description that matches the preview. It was Megatron vs. Optimus and it looked like Optimus Prime was going to sacrifice himself but I think the episode ended before we saw what happened. Any thoughts, and did it air on it's normal time on any markets you know of>