I want to make a game derived from an existing game. That game is owned by a live company.
How do I go about contacting the rights owners correctly and negotiating for the rights to the content?
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Are there any legal ways to acquire the rights to make a derivative video game?
Yes, it's frequently done.
The game is owned by a live company, so how would I contact them correctly and negotiate for the rights to the content?
Find their contact information on the web. Typically with a "Contact Us" page. You're likely not going to find a "Use this number to contact us about making a derivative game". Find their main contact number and work your way through the channels. You may not be able to talk to anyone about it, they might reject you before then.
What are some different deals that we could make?
Lots, or none. Depends on what you have available to offer and what they're willing to offer.
IP can get EXPENSIVE, and it gives a third party way to much control over your game (including, potentially, an expiration date).
Ever heard of Starwars Galaxies? It was pretty infamous for two reasons. 1) [unrelated] they nigh-completely changed their gameplay well after release. Was not well received. 2) They shut down for no apparent reason.
The reason however isn't all that hard to deduce.
Only 5 days later.
In fact, I understand that the then-president of SOE (the devs behind SWG), John Smedley, SWORE OFF others' IP as a direct result. Someone else shut one of his games down, and he had no say in the matter, no recourse. "Take this corncob, right where it'll hurt most. Oh, and take the blame for shutting your game down so it doesn't hurt the sales of the next one."
I can't imagine why he'd be upset by the experience.
On the "up side", the game industry has a Long and Storied history of "borrowing ideas" from one another. iD made the first FPS. To some extent, everyone who made one afterwards was "ripping them off". If you want to mimic gameplay, go for it. You can't patent/copyright/etc GAMEPLAY.
If you want their characters, backstory... not so much. Still, it's not that hard to make up your own similar characters. Superman (DC comics) knockoffs: Marvel: Gladiator, Hyperion, Sentry. Image: Apollo (who is (was?) married to "Midnighter", their Batman knockoff, good times!). Gladiator even has the same "last of his species" thing going.
Other Peoples Intellectual Property can be an "I Win" button for initial sales. OPIP can also be a boat anchor around your neck, dragging you under.