No, it was not in the contract. The deal was between GT Interactive and Take-Two. 3DR was not part of it. Here is the whole story:

http://www.gamesindustry.biz/articles/duke-nukem-dev-3d-realms-not-closing

In this link they mention that 3dr still has "certain rights" to publish DNF. Whatever this means.
And they talk about re-grouping the dev-team.

Yeah, I read an article of rockpapershotgun.com about this also. Seems you might be right there.

Actually, the whole thing is getting more confusing now. I do think Take-Two owns at least something:

"Over twelve years later, its development team was let go due, according to 3D Realms, to a change in the game's publishing agreement that left the studio unable to pay its employees."

.. pretty strange for such an independently operating studio if you ask me.

Of course, then there's the fact court ruling; "The court denied Take-Two's request for a temporary restraining order."

Recently Miller claimed the 12 million dollar was never paid. He was implying there was a contract, but Take-Two just never came through with the money. Of course, because it has been an indirect contract, 3DRealms can still do as they please with their franchise I think. Good for 3DRealms actually and it makes sense they never received the money (as GT Interactive would have gotten it anyways).

The weird thing is that despite sort of an official statement that 3DRealms is no more, they are still alive and kicking. They just had to 'send people home' as they have no money anymore for DNF development.

To be honest it is starting to look like a marketing thing after all. The very moment a bag with money arrives, they'll be back in business as usual, just mark my words.

He's back:
http://www.youtube.com/watch?v=3CwHzclyYnI&feature=player_embedded

3D Realms isn't closing. They've still got lots games in production in some form or another.

you gotta be shittin me...

Haha I had the same reaction!

The IP itself is too much worth to let it die.
(like a maturing wine)
Some studio will develop it soon or later.
And release it when its done.

Even if its crap, people will buy it, simply to
finally have bought it...

They should somehow get their things together, and
sell the IP to a studio that can create the game.

The graphics, effects (the explosions for instance) and sounds are really bad IMO, it looks like 2005. Is this a current gameplay video or fan-made? I don't get it...
The gameplay looks below-average, too.

EDIT: When he is close to a weapon on the ground, the message
"Press ( ) to pick up..."
appears. What is the red ( ) in the video? It looks like the (B) Button from a XBox 360 controller.

But this video really reminds me on the old Duke experience. I like it.

The gameplay is ok, it is a shooter, what else do we expect from a shooter? I only hope that the hero will not heal automagically when taking cover behind a crate like these modern shooters do. This is such a crap, just to satisfy the mainstream.

that is so true. unfortunately.