Unbeknownst to Dimitri, Clive was the one pulling the strings of the scientists kidnapped to work in the research facility. As noted by the large supplement of weaponry found in the lower levels of it, the facility is revealed to not truly be used to build a time machine, rather for the construction of Clive's Mobile Fortress to enact his revenge.
Professor Layton and his company search the building after Dimitri had fled the Towering Pagoda. From talking with Horace, who went with the crew to look around the facility. It is revealed that the laboratory here is where Dimitri Allen had taken the scientists he kidnapped to work on his Time Machine. Those working in the research facility were able to roam certain parts of the city, however. But, before the crew made it to the Time Machine Room, they ran into The Family, who were going to stop them. Luckily, Celeste was able to save them, they then escaped from the facility. Afterwards, they went to the Thames Arms.