Take Two has a publishing agreement with 3DRealms (and continues to have it, despite the current state of 3DR and DNF). In brief, the agreement states that if DNF comes into existence, they get to publish it. The agreement as it currently is doesn't obligate the publisher to give a cent to 3DR in making the game -- the reason for this is because 3DR was an independant developer, and George Broussard/Scott Miller don't like it when they're told when a game has to come out. They were able to self-fund the game over the last 12 years, and because of this their classic "When it's done" approach couldn't be touched by the publisher. At one point, 3DR was offered bonuses for completion at a certain date which they obviously missed.
Take Two couldn't have been more out of the loop with DNF. At one point, they didn't even know what engine the game was running on and mistakingly suggested it was on Doom 3. A lot of people (including the press) make that mistake: It is, and has been for a very, very long time, a modified (heavily modified) version of the Unreal 2.x engine.
An IP is just the idea, characters, themes/storylines, etc. In this case, it's Duke. 3DR owns the game, the idea, etc. -- and they won't give it up. They won't sell it (because they still make money with it, I believe). They won't give it up nomatter what, not even for the quick buck that might've actually saved their game. That's, er, dedication.
Take Two told them to fuck themselves when George showed the latest build and asked, for the first time, for an advance so they could complete the game. Honestly, if I was Take Two, I would've said no. But as a gamer, I couldn't be more infuriated by the choice -- I honestly think if they had the money, they could've wrapped that fucker up.
Now there's no way they didn't already explore their options before closing. They were probably in touch with companies like EA -- trying to save the game. From what I know, they didn't find anything viable in time.
But that doesn't mean DNF is done. It means that 3DR is. The game is still there, and with a LOT of luck and perhaps a little help from communities / developers / publishers who have an altruist bone in their body, it'll happen. It needs to happen with Bob, though. Bob needs to come in and say "this sucks, we're cutting it" and ensure those milestones are reached. If someone gets the publishing rights away from Take Two (who clearly doesn't care about the franchise anymore), then 3DR might be able to reform, hire a few of the original developers, and finish the game.
If George Broussard and Scott Miller don't look for ways to do this, or to help it along -- or they just give up at this point -- then they deserve everything that's happened to them. DNF is very much a legacy of love, as normal developers would've canned the game long ago. They are nothing if not persistant. Hopefully their persistance persists.