The Manhattan Project was the project that developed the first nuclear weapons, resulting in the bombs that were dropped on Japan, effectively ending World War II. The title is never mentioned in the lyric, but is filled with references to the nations racing to build the bomb and when it was finally dropped. The "Enola Gay," as mentioned near the end of the song, is the American plane that carried the bomb that fell on Hiroshima.
Rush is unusual in that their drummer, Neil Peart, writes their lyrics, which are interpreted by lead singer Geddy Lee. It took a while for them to get on the same page with this song. "I wanted the delivery to be like punctuation, and the chorus had to be more passionate and more rhythmically active," Peart told Bruce Pollock. "It was hard to express exactly how I wanted it. The first time we worked on the music, they had phrased the lyrics in a very slow manner and I had to protest. The phrasing of the line was two short lines and then a long line and two short lines and then a long line. There were internal rhymes and internal relationships among the words and within the delivery that had to remain intact for it to make sense at all. It was so carefully crafted that it couldn't be delivered any old way."
Geddy Lee explained to Guitar Player magazine, April 1986, "Sampling isn't perfect enough so that you can make it completely realistic - you still can't get the feel, because digital recording of a sound gives every note pretty well the same value, which you never do when you're playing a lick. On 'Manhattan Project,' Andy played sort of a fretless-sounding bass line on a Roland JP-8 keyboard synthesizer. It sounded great, so to do it live, we sampled that JP-8 sound into my Emulators. So it worked, but it didn't work at the same time. I use it live and it sounds okay, but every slide has exactly the same value, which you would never want. When you play a fretless part, you slide through some notes and pass through others at a different rate. You can't really do that with a stored sound, unless you have a complex sampling situation where you sample each note differently. So, it has its drawbacks, fortunately for us bass players."
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