Freeze-Frame Revolution by Peter Watts

Graser

Far future science fiction novel. Sunday, our lead character, is on an asteroid that has been made into a giant spaceship. The ship is on a mission to build a series of wormhole jump gates all around the galaxy. Naturally, this is going to take some time, like zillions of years, so Sunday and all the rest of the crew spend most (like 99.999%) of their time in suspended animation. The A. I. (artificial intelligence) brain that runs the ship revives a portion of the crew whenever it's time to build a new gate, something about human brains being better able to cope with unexpected phenomena than the computer.

This mission has been going on for a while (zillions of years) and some of the crew start to notice that not everything is as copacetic as they have been led to believe. In particular, it seems that life support for a small fraction of the hibernating crew (3,000) was cut off and they all died. When they ask the A. I. (Chimp) about this he claims he does not know anything about it. Well, he's a computer, if the data that recorded such an event was erased, he wouldn't be able to remember it even if he wanted to, would he?

This prompts Sunday and a few of his / her (hir gender, nor any of the other characters, is never made clear) cohorts conspire to destroy the A. I. This is going to be a bit of a trick because the Chimp has sensors  almost everywhere. He has a neural link to every person on board. Further, the ship is riddled with computer hardware and since Chimp can relocate himself as he sees fit, there is no telling where the Chimp resides at any time.

To evade detection, the conspirators set up a music school / club where they write music. They encode their messages / information using special notations in their musical scores. They might even have written them out with paper and ink to further remove them from the Chimp's purview.

The conspirators are finally able to locate the Chimp by measuring the latency of signals being sent to it.

The ship is powered by a small black hole. Each wormhole they create is also powered by a black hole, a black hole that they create on the fly by aiming a bunch of grasers at a target (presumably a small ball of matter). This process is akin to setting off an atomic bomb. Each graser must fire at the exact same time otherwise bad things will happen.

The conspirators have deduced that the Chimp resides near the chamber used to build the black holes for the jump gates. Changing the firing parameters for one graser will result in Chimp's destruction. Cool. Except things go wrong and a couple of here-to-for unknown players enter the scene. One of the key conspirators has a secret agenda that upsets the applecart. Another is a person I don't remember, he may have shown up earlier, but it's been a while since I started this book and I don't remember him. Anyway, he's got another agenda. The third is a computer program whose existence was never even suspected. It has been dormant, just waiting for the shit to hit the fan.

So all this happens at the very end and it's a little confusing as to just who is trying to accomplish what. The production of the black hole was successful, as usual, but because of the sabotage, they have lost control of it and it takes off on a course orbiting the black hole that powers the ship. Because it is so small (microscopic even) and so dense, it just blasts through everything leaving destruction in its wake. 

The survival of the ship would seem to be in doubt. Chimp coaxes Sunday to enter a hibernation chamber.

Goodreads has a page about this book.