I know it sounds like I'm cheating by putting a licensed game on this list. But even still, it retcons a previous story, so yeah, in my eyes, this one counts.
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#3
Suggested by
Andrew Haase
Where Was Giovanni? - Pokemon Heartgold and Soulsilver
11
Andrew Haase
1 months ago Report
There was an in-game event which explains Giovanni's whereabouts during the events of the game, as well as some revelations regarding our rival.
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#4
Suggested by
Andrew Haase
De-Canonizing Soulcalibur 5 - Soulcalibur 6
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#5
Suggested by
Andrew Haase
Multiple - Twisted Metal Series
00
Andrew Haase
1 months ago Report
This franchise retcons itself so much and no one cares. From to OG to Black to the 2012 reboot, it's almost a new person with each game.
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#6
Suggested by
Andrew Haase
Resetting the Timeline (Twice) - Mortal Kombat (2011) and Mortal Kombat 1
00
Andrew Haase
1 months ago Report
Mortal Kombat (2011) decided to start over with a fresh slate. Until Mortal Kombat 1 was released and did it again reminding us that keeping up with continuity is a sysiphean effort. MK1 has new god, Liu Kang rewrite history to be kinder to his friends and allies, but of course, we can't have nice things and that timeline is also threatened.