Alpha Protocol, won't be receiving a sequel. In an interview with CVG, the executive plainly expressed, "Let's speak very commercially; the game hasn't sold what we've expected, therefore we won't be doing a sequel." He continued that the game didn't have enough to get into that "upper echelon" of RPGs, because the amount "you need to invest to get there is so large because RPGs are naturally big projects."
The Obsidian-developed game suffered numerous delays, alleged tweaks and eventually launched this year to middling reviews (across the industry). It seems Alpha Protocol will have a future akin to that other oft-overlooked espionage classic: Leonard Part 6.