Obsidian's quirky espionage RPG Alpha Protocol is the latest to be de-listed from Steam. The game's store page confirms that it was removed from sale at the request of the publisher, Sega, whose rights for the game has expired. While no longer for sale, players who bought it during its nine and a half years of availability can still download and play it, and keys from other sellers should still work. While much maligned at launch and best played with a gamepad back when such things were unfashionable, it was a sneaky RPG well worth experiencing at least twice.
Update: Sadly, the reason for de-listing the game is as mundane as it gets. As reported by cheery RPS fan-site PC Gamer, Sega's music licenses for the game had expired, and while Microsoft have purchased Obsidian, Sega still hold the Alpha Protocol rights.
While just speculation on my part, the game's removal from Steam seems likely related to Microsoft buying out developer Obsidian, and potentially taking the Alpha Protocol rights with them. Hopefully this means that the game may return at some point, or -- wishful thinking, I know -- get a sequel or other revival, but at least not all hope is lost. While undeniably buggy, poorly balanced and with only half-functional mouse and keyboard controls that rendered several mini-games nigh unbeatable, it still had a lot going for it, as Alice Prime explains here.
Released in the same year as Fallout: New Vegas, Alpha Protocol was Obsidian's big experiment in having a smaller but more reactive story. It was an RPG wrapped around a sub-Metal Gear stealth shooter. Opening and ending sorties aside, its handful of missions could be tackled in any order, and your dialogue and combat decisions would fundamentally alter both future options and how folks perceived you. It was possible to convince just about every enemy to just take their money and leave by the end, or anger a nemesis so much that he'll abandon his mission just to try to murder you. It's a game that had to be replayed to be fully understood, as you're only seeing a fraction of the possibilities each time.
While Alpha Protocol can no longer be bought directly from Steam, keys can still be activated. Gamesplanet are running a while-stocks-last sale, slashing it down to £2.50/€2.81/$3.16. This might be your last chance to pick it up legit. I'd also recommend the PC Gaming Wiki's Alpha Protocol page for an unofficial patch, tech tips, INI tweaks and workarounds for technical issues. While I've not tried it myself, there's a small re-balance mod on Mod DB that claims to reduce the bullet-sponginess of bosses. Probably a good idea.