I have never heard of that, What are you coinjecting the Cas9 mRNA with?

You're RNA could be bad but it's more likely there is something in your injection mix that has gone off. which is what the person above is getting at. Also, are you injecting the same amount of Cas9 every time? like do you actually measure the amount coming out? If you're just eye-balling it, it could be that you're injecting way too much without knowing it.

The injection solution consists of Cas9 mRNA, one gRNA, nuclease free water and phenol red dye. The concentrations for working solution haven't changed, and the injection volume is roughly .14nL (usually some deviation from this as the measurement is calculated using a micrometer.)

This is the equivalent to the "is it plugged in" question. But uninjected or control animals survive? Anyone else in the lab seeing the same die off? Maybe its your fish/embryo water?

I would make new mRNA and anneal some new guides (depending on your procedure) and try it again.

Unfortunately I'm the only individual using the CRISPR system in my lab, so I don't have anyone to compare results with. My plan was just that - to resynth everything/clean up the environment and see if the issue persists. Is there a different method other than [gel electrophoresis to confirm product size and spec to assess concentration/absorbance ratios] that I might consider to determine whether an RNA sample is pure? Hypothetically, could there be some biochemical trickery that could be happening to the RNA products somewhere along the line that facilitates some immune response? (e.g, like in this recent study where 5'-ppp gRNAs produced via in vitro transcription trigger RNA-sensing innate immune responses in human and murine cells, leading to cytotoxicity: Article CRISPR RNAs trigger innate immune responses in human cells

Maybe it would be interesting to see this study replicated in non human cells. Anyway, thanks for the tips. Back to the bench it is.