9. Child Of Light
The Phoenix Saga is one of the most well-known and popular X-Men arcs, and the animated adaptation is equally epic. The five-part storyline was brilliantly done, taking the X-Men off-world and into the heart of a cosmic crisis as they try to stop D'Ken from getting his grubby hands on the M'Kraan Crystal. This would give him the power to rule the universe, and 'Child of Light' sees him eventually cause various disasters across Earth when he finally has the crystal in his possession.
This is a particularly gripping episode that captures all the excitement and operatic qualities of the comic, and because this takes place in the series' third season, viewers have had plenty of time to form a bond with the characters. This makes Jean Grey's sacrifice all the more powerful, even if those with any knowledge of the comics know she'll be back.
While the somewhat bizarre space-based shenanigans are unlikely to be to every viewer's taste, this was a massively important part of the characters' ongoing story, showing the high price sometimes demanded to be a hero.