DunDunDunpachi
Banned
Stardock's link for the DMCA
Stardock's Q&A explaining their own side
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Series creators versus current franchise holders. Obviously, both parties have far more details on the matter than is available publicly.
On the one hand, it could be argued that Stardock did its best to avoid any infringement and is being burned by two petty creators. On the other hand, it could be argued that the creators have been pushed into this decision by the flagrant abuse of the copyrights held by Stardock and the publisher should never have proceeded with the game before resolving the open case.
The timing on the case is important: prior to Stardock announcing Star Control: Origins, Paul Reiche III and Fred Ford announced Ghosts of the Precursors, a game they said is a direct sequel to Star Control. Stardock struck back by issuing a Cease and Desist, claiming exclusive rights over the property.
The removal of the games doesn't indicate the validity of the DMCA (which will now have to be argued in legal proceedings between the two parties). Storefronts typically honor a DMCA takedown request and then let the license holders fight it out. This allows storefronts to host content without being held directly responsible i.e. as long as you respond to DMCAs you can't be directly sued for content that infringes upon someone else's copyrights.