After Gym 5, the Professor goes missing, to be replaced by his daughter.
As previously mentioned, the Rival is part of the evil team. After Gym 7, you go off to stop the evil team, fighting the Rival, the Leader and then the Legendary. The Leader says something about how the Evil Team will never die.
After fighting the Elite 4 (who each have 4 Pokemon), but before fighting the Champion, your Rival appears, and challenges you. After that you find the Champ is the Prof, as already established. He reveals he was working with the Evil team, becoming the Champion to allow behind-the-scenes manipulation. He also reveals at some point that he allowed the Rival easy access to you in hope that he would be able to weaken you.
This next bit is up for some debate. After fighting you (with a suspicious 5 Pokemon), the Champion reveals he has total control over League affairs, and challenges you again with another, completely different team. After this, the police come in, arrest the Champion, and some plot-important guy comes in (ex-champ?) and puts you in the Hall of Fame.
The basic reason for this plot is to try to surprise the player; in Red and Blue, there was no indication there was a Champion until after beating Lance. I really think we should make a huge twist in the Elite 4 for this reason. Black and White had one.
Thu Oct 09, 2014 4:27 am by ReFrostE
» Dimafo140;the foreign guy
Sat Jul 13, 2013 2:32 am by King Dedede
» Time to do some bro stuff
Sat Jul 13, 2013 2:23 am by King Dedede
» a Celebi based story line
Thu Oct 18, 2012 1:46 am by Celebifollow
» Are we going to have access to other regions?
Sat Aug 18, 2012 8:28 pm by treecko's awesomeness
» Is anyone still here?
Fri Jul 27, 2012 9:16 pm by Gelatino95
» Hi guys I'm andrew as you can probably tell
Wed Jul 25, 2012 10:57 am by andrewdoo900
» New Move: Whisper
Tue Jun 12, 2012 5:17 pm by Itsme
» Silent voice or Phonetic wave
Tue Jun 12, 2012 5:14 pm by Itsme