Lusus Flagship is quite large, and relatively dangerous in some points. This is the second level with the C4HD, and it is growing more common at this point. When they appear with IDRs and Sniper-RFs, a combination which is already dangerous turns deadly. However, there are several useful powerups, and a teleporter, to help you defeat them.
You must first destroy a control panel near the back of the ship, and then find the blue key. From here, you need the yellow keycard. It is enclosed by a wall at first, but there is a way to drop it. There is a complex trigger network leading up to the Red Keycard.
Proceed with caution - moving too quickly could plunge you into a situation which you have no way of controlling.