Thousands of Doors takes place between 64's ending and its epilogue.
The Stellarvinden, aware of the threat the Queen of Shadows posed, sent Mario out to collect the Glass Stars and stop her. This caused the War to escalate even further and the Stellarvinden to go unopposed, supported by Peach saying the world will be facing a terrible darkness even after the Queen's defeat.
Thousands of Doors is going to get a remake.
Simply put, Fatguy703 is going to take the remake of The Thousand-Year Door and give it the same treatment he gave the original.- It certainly could happen, given a remake to TTYD was announced for the Switch in September 2023's Nintendo Direct...
