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I have only seen a few episodes of the cartoon "X-Men: Evolution" on YouTube, and it seems that the story arcs are all mixed together.
I saw a bit of a story arc involving Apocalypse in which he causes Magneto to destroy a spider which was a guardian to prevent his release. I also just saw season 4 episode 1 on YouTube in which Apocalypse seems to kill Magneto (and Mystique).
Does anyone know all the episodes that make up this story arc?
Here's an Episode List (also from Wiki) and Stan is correct in pointing out they are streaming on Netflix. But to answer your questions about the Apocalypse story arc and how "the story arcs all mixed together," it's actually a really well executed and interesting arc (elements of which subtlety connect back to prior seasons).
What was good about Evolution is, like the comics, there are a lot of slow burn arcs. The one leading up to Apocalypse does start way back but the episodes to watch are:
S02 E12 "Mindbender" First appearance of Mesmero - Foreshadowing of Apocalypse and opening his first gate.
S03 E09 "Under Lock & Key" Magneto finds out about the three keys that can free Apocalypse.
S03 E12 "Dark Horizon – Part 1" Mesmero wants Rogue to give all of her stolen abilities to Apocalypse to awaken him.
S03 E13 "Dark Horizon – Part 2" The X-Men, Brotherhood, and Acolytes track Apocalypse to Egypt.
S04 E01 "Impact" A Mayan pyramid takes on a technological appearance and an impenetrable force shield surrounds it... meaning Apocalypse-tech.
S04 E05 "Uprising" Foreshadow events in Apocalypse finale- Nick Fury of SHIELD orders new improved Sentinels.
S04 E08 "Ascension – Part 1" The Big Battle with Apocalypse and his horsemen
It all makes even more sense if you watch the entire series arc from beginning to end because you'll see the small clues here-and-there of how things will go... Enjoy!
The last two episodes of Season 4 cover the actual story arc itself. If you're looking for footage of Apocalypse fighting the X-men, that's where you'll find it.
However, Evolution did drop a lot of build-up leading up to the actual story. The setup occurred in the season finale of the previous season, Season 3, which of course is resolving several previous episodes worth of build-up. It's generally a good idea to watch the series in order, start to finish; at 52 episodes, it's a bit of a time investment, but not nearly as much as some other shows. That will give you the whole, complete plot of the show, which differs in some major areas from the relevant comics and other adaptations.
