Now it's time to get a proper fleet again.
Defeating the Vaygr Raiders
What a surprise, the Shipyard Nabaal is under attack by the Vaygr! They're pulling no punches, with a Missile Frigate, and a Missile Corvette and several Bomber and Assault Craft squadrons pounding it for all they're worth. The Mothership and the Shipyard will start pretty far apart so begin the long and tedious task of moving your Mothership towards the Nabaal. This will be useful later on. All your Bombers should concentrate on the Missile Frigate, your Gunship(s) should attack the Assault Craft and your Interceptors should attack the Bombers and Missile Corvette.
You should start off by building enough Resource Collectors to raise your total to at least four, then do as Fleet Intelligence says and construct a Mobile Refinery, then send it to the location highlighted (that should also be where your Resource Collectors go). Once this is done you can construct a Platform Facility which can then be used to construct static Gun Platforms with which to defend your Forward Resourcing Operation (sounds fancy, doesn't it?). A platform can be moved once, after this it can no longer be moved and will remain in that position until its destroyed (these don't even warp with you when you hyperspace out). Send three Gun Platforms to defend your Forward Resourcing Operation (FRO), as this will be important later.
Interestingly enough, try to leave one Assault Craft/Bomber (not squadron, individual ship) attacking the Shipyard, and once there are only that many remaining attackers, move all your ships out of engagement range. Why? Once you've destroyed all the attackers, there is an invisible timer which counts down to the arrival of the main Vaygr attacking force in this battle, which consists of three Carriers and numerous Fighters and Infiltrator Frigates which you are currently not equipped to deal with. Build two Gunship squadrons and two Pulsar Gunships to raise your total to at least two of each, and build another Bomber squadron. By the time this is complete, your Gun Platforms should be in position, and the Mothership should be closer to the Nabaal. To prepare for the next bit, construct a few more Gun Platforms and dot them around the Nabaal. By this point you will have probably accidentally killed off the last few attackers and the game will advance anyway, but if you haven't, do so by moving in your fleet.
Repairing the Shipyard
If you've done this right, the passive repair rate of the Shipyard will be high enough to exceed the damage being dealt to it by the one remaining attacker, which saves time as the next part is researching the Repair ability for Resource Collectors, constructing some, and sending them to help repair the Shipyard. You don't have to fully repair it before it will transfer control of a Carrier to you, which will be already equipped with a Frigate Facility. Start constructing two or three Flak Frigates with it, and if you have enough RUs, construct a Frigate Facility on your Mothership.
Shortly after this some Vaygr probes will appear. You must destroy these quickly, else a lot of pain is going to come your way. One is a little way out from the Nabaal, the other is near your FRO. Send three Interceptor squadrons and a Bomber squadron (Elite if you have one) to deal with the probe by your FRO (this is important) and just the single Interceptor squadron to destroy the probe near the Nabaal. The Vaygr will shortly warp in a Carrier with two Lance Fighter and three Laser Corvette squadrons to attack your FRO - this is what the Gun Platforms and Fighter squadrons were for. Send your Bombers to attack the Fighter Facility on the Carrier, whilst your Interceptor should attack the Fighters and Corvettes that go for your Resource Collectors and Mobile Refinery. Don't expect your Gun Platforms to last long, but they might take a few attackers with them.
You may very well lose your FRO to this assault, so send the Resource Collectors you used to repair the Nabaal to the asteroids not far from it to maintain an income of RUs. Shortly after the forces start attacking your FRO, Infiltrator Frigates and some assorted Fighters and Corvettes will begin attacking the Nabaal. Infiltrator Frigates basically hover over it and a turquoise bar will appear underneath the Shipyard's health - when this fills up, the Shipyard will become Vaygr-controlled. Marine Frigates will then become available for construction in case of such an eventuality.
Stop the Shipyard Infiltration
Resisting the Attack
After a while three Vaygr Carriers will hyperspace in, and Fleet Intelligence will tell you to eliminate them. For once, don't listen to what it suggests because if you do and send you fleet to attack it, the Vaygr forces will overwhelm you as they pour out of the Carriers. Keep all of your ships back, defending the Shipyard as Infiltration Frigates try and board it. Build lots of Bombers for this point, including a Fighter Facility on the new Carrier you have if needed. If the Carriers just sit there producing Fighters, send a squadron over to provoke them, then bring it back. I cannot stress how important it is that you wait for the initial rush of Vaygr to be picked off, because if you forge straight in you will lose every time. By now you will likely be out of RUs, especially if your FRO got destroyed, so it is imperative that you keep as many ships alive as possible.
Any ships you do build during this phase of the mission should be exclusively Bombers, Gunships or Flak Frigates, as you will be attacked by copious amounts of Fighters - ordinarily sheer number would overwhelm you, but with a healthy supply of these ship types any Fighter assault will get minced before it can do any damage, leaving your Bombers free to either help destroy Infiltrator Frigates, or go to a Carrier and destroy it. You should focus on one at a time, and send some Flak Frigates to it as the other Carriers will send lots of Fighters to destroy your attacking forces. It gets a lot easier with each Carrier destroyed, so don't worry.
An alternative tactic is to build one or two Marine Frigates once the opportunity presents itself and use them to capture the Infiltrator Frigates that the Vaygr are sending to capture the Nabaal. This not only neutralises the threat but adds a free ship to your armada (admittedly, not a very good one, but it's better than nothing). You can do this up until you reach your maximum allowed number of capture frigates. Any ship that is Frigate-class or above can be captured, with larger ships taking longer to capture. Also, the ships being captured cannot resist capture, in order for it to stop all capture frigates infiltrating the vessel must be destroyed by defences or other ships. This is a very useful feature, especially for dealing with lone Destroyers or Battlecruisers later on in the game.
In Case of Capture, Break Glass with Frigate
If the Nabaal is captured, Elohim (the commander) will barricade himself in the control room and start the self-destruct sequence. Once this happens, you have five minutes to recapture it before it self-destructs and you fail the mission. At least two Marine Frigates/Infiltrator Frigates will be necessary to accomplish this in the allotted time, not to mention resisting persistent attack from the Vaygr, so if it looks like you're going to lose the Nabaal, bring any capture frigates you have back to deal with it.
Once you've recaptured it, you will confer control of it back to Elohim, but this does not stop the Vaygr from trying to capture it again; as long as there are Carriers to produce Infiltrator Frigates, that threat will remain.
Onwards to Gehenna
When the last of the Vagyr have been defeated in the proximity of the Nabaal (there may very well be Vaygr ships elsewhere on the map) you'll detect a Mothership-class vessel hyperspacing in. Thankfully, it turns out to be the friendly Bentusi, and their incredible Harbour Ship. They will tell you about what fate has in store for you, and instruct you on where to go next; the asteroids of Gehenna. The Nabaal will remain behind, and you will Hyperspace out to Gehenna Outskirts.