There are 6 chips that you need to insert into various slots. Three are accessible without any help - one near where your get the chips at, one in a wedge shaped room, and one in the fuel bay areas.
To get to the other 3 locations, you need to destroy the mainframe. This is near the wedge-shaped room, and has 8 eight switches that you need to destroy. Destroying these will open up the rest of the level for you.
The other 3 chip insertion points are located at another wedge-shaped room, now accessible on the upper levels, in the far back of the room across from the hall with the mainframe, and in the room on the far right of the map, where the terminals initially stated that the mainframe was.
The Jugger factory can be taken down by getting through the room with 3 Juggers, and up to the control room. After tagging one switch, another switch will be revealed, which you should punch, destroying the factory.
The lasers are on the upper level, accesible after you destroy the computer and inserted all chips. As stated, hit the laser switches over and over again (after opening the viewscreen doors) until the ship is destoried. The exit terminal is the large computer screen nearby.
There is a secret term in the back of the ledge in the Mainframe room. You'll need to grenade jump to get there.