Do you get a DOFF rewarded for completing the Klingon Bioweapon assignment chain?

Which faction, Fed or KDF?

Not that I've seen.

Heh, sorry, that was fed.

20h after succesfully completeting Establish First-In Colony I'm not getting the Fortify Colonies mission to show up...

It definitely isn't guaranteed to show up as soon as the mission completes. There are several parts of the chain that I have yet to see short of receiving an invite to someone's bridge. I'm not saying it can't happen. I got my B'Tran blue and purple missions one right after another but that's where my luck ran out, lol.

Just like any assignment, it's not always there.

Chains are doubly annoying - you need to be on the right step AND it needs to be there. This is why focusing on one colony is a pretty bad idea, waiting for steps will take forever.

What I do is check them all once a day, and keep a text file with my current chain status, just the name of each cluster and how many chain steps I've done in it. Copy/paste of it:

Betraka: 6
Affihir: 5
Khazan: 4
Delta Vorlanis: 4
Arucanis: 4
D'kel: 3
Rolor: 3
T'ong: 3
Zenas: 3
Eridon: 2
B'tran: 2
Hromi: 2
Eridan: 1
Azlesa: 0

ok Fortify Additional Colonies showed up in the sector I am trying to get (rolor nebula) with the requirements as stated in the guide (10 shield generators etc etc) but it does not come with yellow text saying completing it will unlock the next one. So is that the right one or is it just similar sounding to the correct one?

Ah, Fortify ADDITIONAL Colonies is unlocked by Fortify Colonies (which actually has the gold text). If you look closely there are a number of missions that are similar to the chain missions but they have text like "reestablish" or "additional". Those are just the repeatable versions but do not actually unlock or continue the chain.

Although I do wonder if repeating them might speed up the chain in some way or even effect the chance of success. I'm not sure how complex the system is.

To quote Heretic, "I wish I could make logic like that in the system."

Creating additional colonies, dropping off more supplies or settlers, protecting the colony, even reestablishing contact when it goes missing entirely don't have any influence on the chain whatsoever.

I suppose the limited unlock system may also be why the chains progress on failure as well as success.

Perhaps you could include what happens when "dismiss" a doff?
And the "Execute for Incompetance" assignment.

Like, "What happens when I dismiss a White Doff? What happens when I dismiss a Rare Doff? Do i get XP or Dilithium? how much?"

"If I execute a Green Doff for incompetence, will I get a 'better' reward from the assignment? What about a Rare Doff?"

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I'll help with this.

Dismissing "Rewards"
White Doff - 75 Dilithium + 10 Recruitment xp
Green Doff - 150 Dilithium + 25 Recruitment xp
Rare Doff - 250 Dilithium + 100 Recruitment xp
Very Rare Doff - 500 Dilithium + 250 Recruitment xp

I'll include some "Execute for Incompentecne numbers when I have some.
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You get the listed rewards, regardless of the Quality Doff that you execute for Incompentnce.
If you Execute a Very Rare, you still get the 'standard' rewards.