The Rise of Ultraman
During a patrol mission in the year 1966, Dan's jet was crushed by Ultraseven's travel sphere. Dan and Seven were both presumed dead by both of their people for years with a memorial dedicated to him in the USP HQ. In truth, Seven took the dying Moroboshi into his ship, though both individuals disappeared after that.
In the meantime, Seven's ship was salvaged by the early USP, who were not able to make use of much of the technology, but were able to create the K-Rays, weapons they would use in their fight against the Kaiju menace.
The consequences for that crash would be felt years later, in the USP's presumption that Ultraman was a dangerous alien, and how Ultraman's distrust of humanity for the presumed death of his brother-in-arms.
The Trials of Ultraman
Back in the world post opening of the Vault, Dan was captured by a local militant group called the Joint Armed Disclosure Front, a group who hated the USP, on the belief that they had engineered the Kaiju now plaguing the world. Their goal was to force Dan into 'confessing', torturing him until Shin and and Kiki came to his rescue. After Shin tranformed into Ultraman, saving him from attempted murder, the group's leader somehow summoned a Kaiju.