I asked about this same issue in a "game talk" thread. Then I raised it in a bug thread. (Search for the word "unarmed" if you want to see those.) You're not the only one.

You might answer a few questions for when someone eventually looks into this:

1. What version are you running, 1.1?
2. Is this happening in a campaign scenario, and if so which one? Or a regular "sandbox" game?
3. What difficulty did you have it set at and what intelligence level was the enemy set to? (I don't think this affects the problem you're seeing, but others will ask and assume you're mistaken and imply you're playing on super-easy and choosing to fight brain-dead opponents.)

EDIT: Whoops! Your subject line answers two of my questions: The difficulty level and that it was scenario 2 of the campaign. Sorry I overlooked that.

For me it happened in several campaign scenarios with 1.1beta4 and 1.1. I don't know the cause or how to fix it. I think that it might only happen in campaign games, or there would be more questions about it. It's also possible it only happens to people who updated with the collectors edition content or something (I did that, and I'm sure not everyone does.) There was some speculation that it had to do with the rate at which the AI designs new ships - that they aren't doing this often enough, and so aren't building ships with weapons. I don't know if it's true, but I thought it was an interesting suggestion.

I think I'm going to set the game aside for a few months while they stabilize it.

There was some speculation that it had to do with the rate at which the AI designs new ships - that they aren't doing this often enough, and so aren't building ships with weapons.

sez Mr Draginol, on yesterday's journal entry:

one of the most intensive things that the AI does is design ships. Part of that reason has to do with the actual graphical assemblage which I don't fully understand what's involved on that part. But I only allow the AI to design ships once per year right now. If I tweaked it to even 3 times a year I think you'd notice a significant difference, especially early on when human players have better ships because in 2226 the human player has gotten plasma weapons and the AI is still running around with laser 1 or something when it has actually researched Plasma weapons as well.

I don´t see why ship design should be the problem. When starting the campaign games the Drengin alredy have laser weapons (easy to check if you open diplomacy screen), so there are no reason why they do´nt put them on the ships from the beginning unless the computer only make ship design after 1 year which sounds extremely stupid.

I forgot to add they were also defenseless. I am running patch 1.1 as well. The first time I played the scenario was with the original unpatched game. They gave me a lot harder run for my money and I was playing them on normal or even easy. I'm wondering if the AI sometimes gets stuck in a rut. I noticed the naked defenders before but after blowing them up the computer always built better ships spanked my butt and sent me crying for my mommy. This time they just sat there and let me exterminate them with no resistance other than the very few armed starbases they initially built.