It is where Lewis was left as an infant where he was taken care of by Mildred and shared a room with Goob. By 2037, in the timeline where Goob became Bowler Hat Guy, the Orphanage had been abandoned and Goob left alone, the building slowly beginning to decay.
In another alternate timeline, the Magma Industries controlled one seen in the video game, the Orphanage still stands and apparently still in operation, though is isolated from most of the old parts of town, surrounded by lava, with Wilbur having to dig a tunnel to the mainland to allow the orphans to escape.
Role in the film
When Lewis is taken to have a better life at the orphanage, Mildred accepts him to be in the orphanage. Lewis grew up with inventions as the age of twelve, but most of his inventions while Mildred is planning an interview with the Harringtons. The interview, however, was unsuccessful due to Mr. Harrington's allergy to peanuts. The next day, Lewis plans on making an invention to help find his mother where he worked very hard on it. Interested upon going to the science fair, Lewis tells Mildred that he is through with inventions as he decides to participate, much to Mildred's worry.
In the future, Lewis and Bowler Hat Guy end up in an altered, closed down orphanage due to Goob having an unhappy future of him not being able to be adopted as the orphanage closes down, planning to take revenge against Lewis. Soon as Lewis plans on not inventing DOR-15, Lewis' future is restored with the Bowler Hat Guy planning to be adopted to have a better future. Later when Wilbur and Lewis travel to the scene from the very beginning of the film, the two look at Mildred giving Lewis a better life to which at the present, Lewis explains the reason why he let his birth mother go is because Lewis already had a family. With Lewis' invention a success, Lewis bids a farewell to Mildred as he finally becomes adopted to have a better future.