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So I've spent hours now looking for a good walkthrough, but I can't seem to turn anything up. Whenever I search, I keep finding strategy guides, which I don't need since I know that aspect of the game inside out - what I want is a complete compilation of all the quests in the game (especially the ones where there's a timed element), and how to make sure you don't inadvertently fail them etc.

So far the only ones I've found have either been incomplete, very poorly organized, or both.
You don't really need a walkthrough. You're free to play the way you want.
You don't have to free all towns, you can ignore all quests given to you with exception of the main quest of killing the queen.
If you know what you're doing you could go straight to her and kill her.

If you do wish to do some exploring first and free all towns, the order in which you do so is up to you.
Drassen is quite obvious the 1st choice, but can be done later. You could go to San Mona first and train your free merc to the max first.

For me personally I do it in this order:
- Drassen
- find the pilot (talk to named npc's in Drassen airport)
- take out the Drassen SAM site
- grab as much stuff as possible and head to San Mona to sell to Tony
- take out the SAM site south of Chitzena
- free Chitzena
- escort the American couple to the Drassen airport
- free Cambria and take out the Hicks
- take the Cambria SAM site

After that, I just go where I think I should go.

Check http://jaggedalliance.wikia.com/wiki/Jagged_Alliance_Wiki for some walkthrough info.
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HertogJan: You don't really need a walkthrough. You're free to play the way you want.
You don't have to free all towns, you can ignore all quests given to you with exception of the main quest of killing the queen.
If you know what you're doing you could go straight to her and kill her.

If you do wish to do some exploring first and free all towns, the order in which you do so is up to you.
Drassen is quite obvious the 1st choice, but can be done later. You could go to San Mona first and train your free merc to the max first.

For me personally I do it in this order:
- Drassen
- find the pilot (talk to named npc's in Drassen airport)
- take out the Drassen SAM site
- grab as much stuff as possible and head to San Mona to sell to Tony
- take out the SAM site south of Chitzena
- free Chitzena
- escort the American couple to the Drassen airport
- free Cambria and take out the Hicks
- take the Cambria SAM site

After that, I just go where I think I should go.

Check http://jaggedalliance.wikia.com/wiki/Jagged_Alliance_Wiki for some walkthrough info.
Thanks for the reply. I've been using the wiki more and more, and it's pretty decent though it could be organized a bit better. The main reason I wanted a walkthrough wasn't so much to find solutions for quests, but rather, to make sure I knew what all the quest triggers and time limits were. To make sure I don't screw something up or activate it before I'm ready to do it. Think I've got a pretty good handle on it now, though knowing my luck I'll have missed one small thing and it'll end up ruining my whole game, haha.
The only quest you need to finish is the one killing Deidrianna. All the other quests are optional.