While reading about the attack on bin Laden's compound, I mentally turned to my character Maggie and asked her if she was ready to be public enemy #1 on the Jovian Frontier.
She looked kinda scared. I don't blame her.
It's an important part of writing a story: making sure the "bad guys" are as real as your heroes. Bad guys need goals and reasons to pursue them. Their actions need to be every bit as reasonable as your heroes' actions. Their pursuit of their goals every bit as determined.
And as they say, one man's terrorist is another man's freedom fighter, so if Maggie is going to pursue independence for Jupiter's outer moons she's going to be labeled a terrorist by the establishment. They're going to act accordingly. If they get a chance to send the equivalent of a SEAL strike team to kill her, they will. Maggie's no combat ninja, so it's scary stuff. Ben Franklin had a great quote (as usual): We must hang together or we will all hang separately.
If I tried to portray the enemy as bumbling or incompetent, it would be difficult to take the story seriously. Even trying to say the enemy consistently underestimates the main characters will hamstring the tension. And an enemy without motivation is pointless too -- how many movies have you seen where the characters head out into some kind of wilderness, immediately trip over some major predator and then get chased across half the planet by that predator, tearing up the landscape as they go? Because predators have nothing better to do with their time, you know. And they have no self-preservation instincts either. Please do some homework on how predators actually go about their business.
In my story, the enemy is the establishment, the one with the money and the intelligence operations and the military. If they don't act like a real government, I'll be making a pretty transparent statement about what I think of governments. And while science fiction has a long history of social commentary (something I support whole-heartedly, even when I disagree with a given story), I don't want to be transparent about it. So competent it is.
Maybe you say but it took us ten years to find bin Laden, that's not all that competent. Maybe that sounds like a long time to you. Maybe it's a long time to live on the run. But I'm getting to an age where ten years isn't all that long anymore -- and I'm much younger than bin Laden. How long do you think it felt, to him?
What's the most sensible thing for your bad guys to do to stop your main character?