Once you enter through the doors, you're in a Star Tours sized simulator with a big screen on the wall, with 2 smaller ones on each side. Monogram appears on the left screen going through basic safety stuff.
Now I'll do a scene by scene description:
Scene 1:
Takeoff from Perry's HQ. You enter a purple vortex when the time travel starts.
Scene 2:
You leave the vortex to dee the great pyramids being built. A caption on the bottom says Egypt,(whatever year they were built) BC. Doofenshmirtz is riding his inator with the kids in a glass cage at the bottom. He speaks for a while, until Perry jumps onto the machine. While fight ing with Doof, the machine spins out of control and hits into the Sphinx with a human body. The body collapses, and 2 builders building it look at each other and shrug. Doof's elbow hits a button that creates another vortex.
Scene 3:
A new caption appears with Rome, 44 BC on it. The 2 continue to fight. In the process, they hit a pillar down. The pillar lands on someone who was about to stab Julius Caesar. Perry pushed Doof into his entire control console. This causes the machine to smoke, and glow green followed by an explosion.
Scene 4:
On the right screen, the 2 are fighting. Perry then grabs Doof and uses a jetpack to pull them into the air. The kids stay put in the cage, while Perry and Doof float off screen. A trapdoor in the floor opens and the two (in AA form) fly into another trapdoor in the ceiling. Monogram appears on the middle screen and tells us that we have goytten caught in the space-time continuum. He explains then that they had taken some of Doof's inators and made a Timefixer-inator. Monogram activates it, the lights in the simulator turn on and he congratulates you on your first mission complete.