UPDATE 20th June 2019: Sega has been in touch to say it still owns the Alpha Protocol IP, and to clarify the game was pulled from Steam due to the expiry of music rights.
Last night, Sega issued a statement saying Alpha Protocol was removed on Steam "following the expiry of Sega's publishing rights". This was incorrect.
Sega didn't expand on its statement about the expiry of music rights, but it probably has something to do with scenes like the boss fight in the video below, which includes Turn Up The Radio by Autograph. Given Alpha Protocol is nine-years-old, re-licensing music for the game probably didn't make much sense to Sega.
The future of Alpha Protocol, then, remains in Sega's hands.
ORIGINAL STORY 19th June 2019: Alpha Protocol has been pulled from Steam after Sega's publishing rights expired.
The Steam page for Obsidian's much-loved spy role-playing game includes the following note:
"Notice: At the request of the publisher, Alpha Protocol is no longer available for sale on Steam."
A Sega spokesperson told Eurogamer the removal had to do with the expiry of Sega's publishing rights.
"Following the expiry of Sega's publishing rights for Alpha Protocol, the title has been removed from Steam and is no longer on sale."
It's worth noting anyone who bought and downloaded Alpha Protocol will still be able to play the game, and anyone who's bought it but not downloaded it, or since deleted it, will still be able to download it at any time. So, for owners of Alpha Protocol, nothing changes.
With Sega's publishing deal expired, it seems Alpha Protocol is now fully in the hands of Obsidian, which is now owned by Microsoft and no doubt working on Project Scarlett titles. Perhaps the game will pop up on the Microsoft Store in due course, and, hopefully, return to Steam.