Over the last two decades, the Duke Nukem franchise has proven to be something of a cautionary tale. The previous original title in the series, Duke Nukem Forever, had been in development hell since at least 1998, starting with Apogee Software and its subsidiary 3D Realms (who developed Duke Nukem 3D) before finally landing at Gearbox Software in 2010. Gearbox had bought the rights to the franchise from Apogee with the understanding that everything would be "free and clear," meaning that all of the copyright questions had been settled, all copyrights and trademarks would belong to Gearbox, and Gearbox wasn't going to get sued by some disgruntled artist down the road.
In September of last year, the composer for the original Duke Nukem 3D score Bobby Prince (apparently very disgruntled) filed a lawsuit against Gearbox over unpaid royalties stemming from the release of Duke Nukem 3D: 20th Anniversary World Tour. Prince's complaint, which also named Apogee as a defendant, stated that Apogee licensed the tracks to the score from him and that Gearbox owed him royalties for using those same songs because Gearbox did not establish a licensing agreement with him.
Since Prince's lawsuit would seem to suggest that Apogee did not turn over the franchise "free and clear" as was specified in the contract, Gearbox has filed suit against Apogee for breach of contract. Gearbox asserts that they brought the issue of Prince's lawsuit up with Apogee, who failed to repay them against it.
This marks the third time that Apogee and Gearbox have gotten into legal entanglements over the Duke Nukem franchise. The first was back in 2013 when 3D Realms filed suit against Gearbox over what it mistakenly believed were profits Gearbox owed Apogee regarding the sale. That suit was later dropped by 3D Realms, claiming it was a "misunderstanding." The second suit was in 2015, when 3D Realms issued a development license to developer Interceptor to create Duke Nukem Mass Destruction, well after Gearbox had purchased the rights to the franchise (and thus being the only company who could issue such a license). The second suit was eventually settled out of court.
Given the history involved, it's possible Gearbox will prevail against Apogee, but may have to reach a new agreement with Prince.