Somewhere along the line, you should have recieved the access codes for the power system.
Go to the bridge, and go to the bridge console. Upload the software, unrestrict the access, and then shut down the power system. You should get a message saying that the shields are down and there are ships incoming to attack.
After that, the docking hatch will be open. Make your way back to where the Ebon Hawke is, and everything should be good to go.