In "It's About Time", the Flynn-Fletcher family visit the museum and see skeletons of their old dog, Bucky, and the man he ran away to live with, Old Man Simmons. Phineas and Ferb find a time machine, fix it, and go back in time with Candace who wants to bust them (she had been thrown out of the museum earlier for yelling, but snuck back in). A T. Rex attacks them, but Phineas contacts the Fireside Girls in the present, by finding the place where a future fossil is, and wrote a message with a stick. Using their Fireside Girls manual they rebuild the time machine. However, because of an error in the blueprints (possibly from inside the manual) it ends up being a tie machine. The fix the error and rescue Phineas, Ferb, and Candace. They also (accidentally) bring back the T-Rex, but it is hit by Doofenshmirtz's Freezeinator, and becomes part of the exhibit.
In "Phineas and Ferb's Quantam Boogaloo", Phineas and Ferb use the time machine there to go into future, and find a tool needed for their project, a thing that fuses metal and wood. In the future it got a new wing added (really just a giant wing-shaped statue added to the top). It is used multiple times again for time travel throughout the episode by Phineas, Ferb, Isabella, Candace, her future self and Xavier Onassis. There is a janitor there who is always dumbfounded by the time machine's disappearance in the present and future.