Let’s go through it by all the numbers though (and as the on-line guide also has it), just to make sure nothing else strikes you as amiss. First, you launch from the depot and auto to Waypoint or Nav 1. There you’ll find a destroyer (which you leave alone) and four Paktahn. After taking out the Paktahn, four Dralthi appear, and you dispatch them.
You then auto to Nav 2, where you find another destroyer and four Dralthi. After the Dralthi come six Strakha. After those fighters are destroyed, if you press “N”, you’ll see that the next Nav point is indeed called #3. You auto there, where you face the usual, irrelevant destroyer and three Darket, followed by six more, all nine of which you must slash and burn. If you then press “N”, you’ll only see references to Nav 1, Nav 2, and the so-called Kilrah area, which is actually your next stop, Nav 4. Nav 3, where you are now, will for some reason no longer be referenced, so I guess this is a data glitch in the game, and also, I assume, why you’ve been saying there are only three nav points.
It is at this point though, after you’ve killed the last Darket at Nav 3 and are still at Nav 3 that you must cloak (Cntrl + C). Only then can you safely proceed and auto to the next point, which, as noted, will be the Kilrah area, where both Thrakhath and Hobbes should be waiting. (The waves of Sorthak that you describe result whenever you fail to first cloak at Nav 3, and it’s then a failed mission; there will be no Thrakhath to kill and no chance to destroy Kilrah.)
Once at Nav 4, you must now de-cloak and kill both Thrakhath and Hobbes, and when you do, the game automatically “deposits” you over Kilrah and then down to the surface where you are able to cloak again.
The other method you can try is what McGruff suggested–cloak as soon as you leave the depot and auto to each waypoint in turn. Of course, it will take a little longer for the “Auto” light to come on at each waypoint since you’ll be passing by all the fighters instead of killing them, but once you get far enough on toward the next waypoint, your radar will clear and you can then auto the rest of the way. When you finally reach the Kilrah area, Thrakhath and Hobbes should be waiting for you.