A multi-galactic civilization is pretty well impervious to any conceivable NATURAL disaster. Nothing short of the complete collapse of spacetime throughout the universe is going to have effects on that scale.
Civilization is always built on social and technological structures that make it possible, and the easiest way to create the kind of chaos that you're talking about is to kick one of them over. Make your civilization completely dependent on a particular technological tool or process, and then have it stop working for some reason.
The best example of this I can think of offhand is from the Hyperion novels by Dan Simmons. In this case it's just a single-galaxy civilization, but the principle is the same. The civilization has spread and built its entire social and economic infrastructure on a technology that allows instant teleportation anywhere in the galaxy. It's so cheap and easy that nobody travels or moves goods any other way. It's been like this for so long that nobody CAN travel or move goods any other way. Then it stops working. All communication between planets and even cities is cut off. Nobody can move food.
It's not even that far Out There as far as Science Fiction is concerned. IN 1859 the Earth was hit with a massive solar flareenter link description here. This caused aurorae to be visible as far south as the tropics, and so bright that people in temperate latitudes could read by its light. Telegraph wires were collecting so much eccess current that they were starting fires.
A similar event occuring today would be MASSIVELY disruptive, because modern society is completely dependent on electricity and wireless communication. A solar event of this magnitude would knock out GPS and satellite communications entirely, potentially to the point of destroying the satellites themselves. Power grids worldwide would go down, potentially for months due to widespread damage to transformers. Distribution of food and fuel would be severely impacted. Depending on the time of year, loss of power would cause significant loss of life due to the sudden loss of the ability to heat homes. And that's not even taking into account the damage that humans might start doing themselves at that point just out of panic.
So, TLDR. Destroy your multi-galactic civilization with panic.