While some of its staff were in 1955, young Biff Tannen stole one of the new DeLorean time machine and began skipping wildly across decades. Doc sent a crew in to follow him and bump him back to the present.
Behind the scenes
The events that led to Doc selling the Institute to Krusty in 2006 were developed as part of The Simpsons universe crossover to explain the history of the building. However, this information is non-canon.