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Basically, the publisher (Del Rey) had set the release of the novel to coincide with the release date for the game that was slated at the time, but when LucasArts changed the release schedule for Staff of Kings to the tune of a year long delay in a harbinger of the whole We're Abandoning The Internal Version To Focus On Force Unleashed fiasco, they did not let Del Ray know. Despite MacGregor's attempts to communicate this development with his editor, the game came out with no book. Rather than release the book even slightly belatedly, it was decided that it wasn't worth releasing it at all (?!). At one point, Howard Roffman (Lucas Licensing exec and interim LEC president) told an inquiring fan the point-blank falsehood that the reason for the novel's mysterious absence was that MacGregor had "missed the deadline," despite the fact that the manuscript had been submitted an entire year before the game came out.
It's completely ridiculous and a little heartbreaking to think that a completed Indiana Jones novel will not see the light of day simply due to a communication failure and boneheaded business decision. I think I know what MacGuffin Indy should be searching for in the fifth movie. For his part, MacGregor seems more flummoxed than pissed off, noting that he was "paid quite well" for the adaptation, but the publisher lost money and us Indy fans are left to cry.
Think you can hold in the tears? MacGregor has this image of the novel's cover to help get you going: