After a short fight, go right to disable the power supply (the fuse box). The current is protecting a crate, inside of which there is a smaller one. Place the smaller crate next to the door, by the glass wall. Thanks to this, you will get inside.
Use the terminal in the office. You will open a big door outside. Exit through the door and go to the helipad. There, destroy the white-and-blue antenna to provide yourself with a spot to jump down.
Start by using the astronaut's box
Down below, first make it up, where there is the astronaut's box. From the box, you will receive dynamite. Use dynamite to blow up the silver box next to the crane, before the submarine. Also, destroy the box next to it and use the parts from both of the boxes to upgrade the crane. Afterwards, use the crane to activate the rocket that you find on the submarine.
The underground hangar
The only door to open... afterwards, go to the upper floor
In the underground hangar, go through the door that you open with the prybar. Climb up the ladder and use the color gun swapper in the neighboring room to obtain the jetpack from behind the glass pane. The jetpack can be used by the astronaut.
Make it over to the balcony, where there is a jetpack icon. You fly jetpack just like you fly the chicken. Also, the jetpack runs out of power, but the use is longer than in the case of the chicken. By flying it into the red activation fields, you can fly it for longer.
Make it over to the top and, after you climb up the ladder, use the jetpack to follow the trail of studs. Activate the terminal and build a dynamite disposal machine. After that, return with the dynamite to the previous position, where the big silver brick used to be.
Build the teleport, collect the lever and mount it above the chasm (before you fly the jetpack, remember to activate the icons on the ground). Go up. Blow up the silver door with dynamite (summoned with the astronaut's box) and walk into the next area.
As soon as you reach the last room with the generator, there are several steps to take: pull the element by the wall, to the left of the generator, using the rope, and rebuild the generator. Afterwards, activate the terminal.
Go right and destroy the crate in front of the grate. Place it by the generator to build the missing part.
Finally, by the grate on the right, fix the fuse box, thanks to which you will be able to jump onto the balcony above. There, you will free the professor by pressing the button. Enter the UFO and escape the location (and end the mission).