How many video games out there have the bad ending, the hero failing, or the villain winning the canon ending?
Link gets killed by Ganondorf in Ocarina of Time, which leads to the downfall timeline of most of the "classic era" games.
None of Raiden's champions were able to defeat the Deadly Alliance of Shang Tsung and Quan Chi, but they along with Raiden get blown up trying to stop Onaga during the beginning of Mortal Kombat Deception.
The 2011 entry of Mortal Kombat starts with Shao Kahn absorbing Blaze's power and is about to finish Raiden off before the latter sends his past self the message "he must win".
Mortal Kombat 1's main villain is revealed to be a Titan Shang Tsung, one who came from a timeline where he won the final battle in Mortal Kombat 11's Aftermath story.
Dragon Quest Builders takes place in a "what-if" scenario where the Hero accepts the Dragonlord's offer of "half the world" while the latter takes over the world and removes humanity's ability to build and create.