It wasn't supposed to be that way. According to a report in Deadline that's now been confirmed by Baldwin and Fox, Baldwin dropped out of the bit after Fox executives nixed a joke about the News Corp. hacking scandal that was slated for ceremony's opening number.
Baldwin confirmed the report on Twitter, saying "Fox did kill my NewsCorp hacking joke. Which sucks bc I think it would have made them look better. A little ... If I were enmeshed in a scandal where I hacked phones of families of innocent crime victims purely 4 profit, I'd want that 2 go away, 2."
According to the New York Times, Baldwin was slated to play the President of TV in the number, and when on the phone with a colleague, said, "Rupert, is that you? I can hear you breathing!"
After the sketch was recorded, Fox execs nixed that part of the bit, and Baldwin thought it no longer worked comedically. He dropped out and was replaced by Leonard Nimoy.
A Fox spokesman confirmed to the Times that they had indeed nixed the joke, because they "take the hacking allegations seriously and did not want to make light of them."