The passenger ship is not AT ruby, but instead is on it's way to Ruby, from the system where you rescued th especial ops team from. It's in the trugati asteroid field, or around there, in one of the uninhabited systems like Castor, near Agena and Adhara and the like. It will jump in just after you jump in, so give it a few seconds before deciding to jump out. There'll be a lot of patrol ships and gunboats, but if you've got a kestrel (or even a modified Corvette like I had at the time) then it should be easy. Watch out though, because the weapon is in one of those weak little ships that VIPs are transported about in, so they blow up very easily. It also jumps out almost as soon as it jumps in, so you gotta be quick, and be sure not to destroy it, or the mission is failed.
To get the Alien missions (which gets you 10mil Credits and access to the rebel ships and technologies) then you have to go down to Sirgil III or Sirgil Starport. They offer you a job to go to Nexus to investigate disturbances, and it follows on from there. NOTE: I recommend getting the tractor beam from the retrieve weapon mission (which I described above) because it allows you to hold the alien cruiser in place while you pound it with your proton turrets or whatever. If it gets away, then the shields regenerate superquick, which makes it important to stay within gun range - missiles and rockets and torpedos knock it away from you due to it's low mass, so just hold it in place with the tractor beam and pound it with guns. It might take a while (it has a shield rating of 1500), but if you stay aout of the way of it's beam, you'll be alright.
If you've still got problems, ICQ me at 57810993
------------------