The first thing Rui did was begin documenting the entire scene, he used the eco-survey device that the Ministry of Ecology and Environment provided to him and carefully used it to collect pictures. He especially documented the refilled hole, extensively documenting it so that it couldn't possibly under-considered when the Ministry went over his reports.
Once he was done, he began considering his options.
The first option was to simply routinely continue his mission according to recommended guidelines, and hope for the best. Ultimately, neither the Martial union and Ministry expected a Martial Apprentice to solve the entire mystery of the mysterious creature all by himself, as long as he fulfilled his duties, he wouldn't receive any backlash.
However, this route reduced the probability of Rui succeeding in completing the mission objectives. Which meant that Rui would not receive the full mission reward if he went down this route, most likely at the very least.