I want to say Xenosaga, but that was 2002.

Golden Sun?

Yes

So let me round this up. 

#47

-Second game in a saga

-Involves some time travel

-Refusal to accept loss leading to acceptance that a mistake was made

-It has a serial killer with a smile

-Rumors

Almost forgot about this thread, time to catch up.

50: Twisted Metal 3 PS1
Lots of good Co-op times on the PS1. But this game was one of the best. The Specials were among my favorites in the series, particularly Sweet Tooth, Thumper, and Club.
49: Twisted Metal Black PS2
Similar to Twisted Metal 3, except this game I also enjoyed a lot solo. Again Sweet Tooth special was quite fun.
48: Command and Conquer Red Alert 2 PC
Common theme for my top 50 games is I likely spent over 100 hours on it, except for recent games. This game is no exception and beating the campaigns over and over again kept me entertained. After beating those, random maps are still fun, implementing funny and effective strategies with the Chronotroops, or brute forcing with a ton of tanks.

47: Hint:This game was also a strategy game on PC. It featured medieval warfare between Crusaders and Arabians. The game was keen on resource management, especially early on.

No one guessed my #48, which was Splinter Cell: Chaos Theory. Someone was about to guess it (you know who you are )

Now for my #47: This was a game from a defunct franchise and a defunct publisher, but from a developer that developed wacky games in the past years.

Clues:

#48 A remake/reimagining of an old classic FPS.

#47 A game where vengeance is finally completed

48: Doom 3 or Wolfenstein TNO?

47: I don't know. A lot of games with vengance out there XD

Correct on 48, but which one? (hint, it wasn't developed by id!)

For 47, vengeance was the central theme for the entire series. Anger is pretty much the only emotion the protagonist shows. 

48: Wolfenstein

47: Maybe God of War 2 or 3?  I haven't played much besides the first one, and my PS2 broke before I could get far.