From the previous mission, you will have been told (and witnessed) the fact that a reactor required to get the base online, is present in the Junkyard. This mission is the chance for the player to acquire it and power up the base.
1) Once you leave the base, Clay will prompt you to head for the Junkyard.
2) As you get close to the Junkyard, Clay will point out the patrols around the yard.
3) You should be able to see the reactor placed close to the junkyard, in order to get the required fuel rods, the player must carefully approach and dock to the reactor to claim them.
4) To do this, you must carefully approach the reactor. The greater your thruster usage, and the closer to the patrols you get, the brighter you will appear to the patrols and so the more likely they will be detected. If you move into the detection range of a ship, Clay will warn you and you will have 5 seconds to get out of range before the alarm is sounded.
5) Once you have successfully made it through and docked to the reactor, the fuel rods will be transferred and you can move off.
6) Once you undock from the reactor, the alert will be sounded and you will have to make a run for it. At this point, you should have disrupters so a useful tactic is to take out as many of the vessels as possible this way before running.
7) Once you reach the Effrit, the pursuer vessels will no longer be able to follow and the mission will be a success.