Well, I wasn't going to respond since it's been too long since I played to offer any specifically helpful advice, but I noticed this on the homepage going without responses for a while, and I thought I'd chime in.  (You are talking about IWar2 right?)

All I can say is that the game suffers from some pretty unreasonable difficulty spikes, and that the most problematic and infuriating one is very early in the game, perhaps just what you're describing.  This was one of my favorite games of all time, but sadly it's been a few years since I've last played, so I can't say I remember the scenario exactly.  I suggest you keep at it, and rest assured that the entire game won't be quite so insane, so it's worth the effort.  In fact, I'd say the bombastic difficulty spikes are by far the worst part of the game, but most of it is pretty reasonable.

Thanks, I was contemplating Elite Dangerous, but my internet connection is not so good.  So I decided to go back to this game, it has been a while for me to.... I don't know if I really finished it earlier.  I really like the first person view, true space physics, yada, yada....   I found a help file I had from earlier and reread it again after posting this question.  It was out of order (sequence), so I was confused but did find the solution but have not had time to go back and continue yet.

The solution was to throw or tow the cargo pods at the star station, they are full of nuclear warheads and will probably go off when the star gun fires at them to protect the base.  Thanks for your reply.  So far this is the best space game made that I know of.

I've been playing Elite Dangerous lately, but I definitely like IWar2 far better in most respects.  Elite feels a little more free roaming, but I hate the cartoonish WWII in space flight model, and dreadfully miss the flight model in IWar2, which I think was probably the best of any space sim.  (Evochron Mercenary's flight model is also pretty good, but certain aspects of weapons mechanics sort of ruin it.)  

In fact, I've been contemplating going back and playing IWar2 a lot recently, but I've been resisting, because it makes me hate the Elite flight model so much that I don't want to play it.  I think I'll wait until I'm thoroughly burnt out on Elite before I can re-experience IWar2, which was, in my opinion far superior.

I went back to iwar2 after playing ED planes in space. It was impossible to get the devs to listen with all the forum noise that the planes in space model was shot. The early beta of ED has near Newtonian model with no flight assist now sadly gone because the real physics made evading combat too easy. I'm really into the iwar quick combat now great fun I can last about an hour in the heavy patcom. Star citizen seems a better flight model than ED but bored of patches and bugs.

Glad to see there are so many others so discontent with the ED flight model.  Indeed, if you mention it on the ED forums, the fanboys will pile on and mutilate you.

I am slowly continuing on with the 'simulation'.  Control of the ship is more difficult to master, but once you get the hang of it, it is much more real.  I wish I had pedals with my stick to control vertical vectors.  I thought elite:frontier was great, I don't think the problems I have is with the flight model, it is more with controlling all the systems.

ED is graphically a big flash, and making it easy for the modern gamers is where the money is apparently.  I was on their forum early in the developement and had the same response from them as you.  I gave up.

I don't have cable internet, I have long distance wifi from the top of the mountain, and ED went the on-line path, so I don't feel my connection is good enough to get a good experience.   I was a little disappointed when they decided to drop the single player mode.  Maybe they will get stand alone on a later beta.

If you get around to playing IWar 2 again, be sure to check out the revived website for mods both old and new, and to get help if you get stuck.

Here is the link:  http://www.i-war2.com/