The final battle against Red featured the team from the original Twitch Plays Pokemon. All hail Lord Helix.
Well, those crazy kids over at Twitch Plays Pokemon have done it again, defeating Red on Mt. Silver thus completing Pokemon Crystal. As an added surprise, Red was not using his usual team of Pikachu, Espeon, Snorlax, Charizard, Venusaur and Blastoise, but the rag-tag team that the original Twitch Plays Pokemon's Red used. Praise the heavens, for Lord Helix has returned!
AJ's final team consisted of only five Pokemon: Steelix ("Solid Snake"), Dragonite ("Katie"), Espeon ("Assassin"), Pidegot ("Brian"), and of course, Lazorgator (Feralgatr). Red's team was Zapdos ("Battery Jesus"), Venomoth ("ATV"), Nidoking ("King Fonz"), Lapras ("Air Jordan"), Pidgeot ("Bird Jesus"), and, the one true savior, Lord Helix (Omastar). You can watch the full climatic battle in the YouTube video to the right.
This time around, only four Pokemon were released: Drowzee, Sentret, Togepi and Wooper, and it took Twitch 13 days, 2 hours, and 27 minutes to finally complete the game. For the record, it took them over 16 days to beat Pokemon Red, which is considerably shorter than Pokemon Crystal, meaning that Twitch has somehow become much more efficient.
As for what's next, true to the creator's word, the game will continue on to Pokemon Emerald, although we may have to wait a while to see it. A counter on the stream says that the Emerald play-through won't begin for another six days, leaving Twitch the freedom to explore some of the game's end-game content.
Source: Twitch Plays Pokemon!