The Op in Aphid, Mr. Bree, and that slimeball Jonas

[ex mechanic]

I think the term "operation aphid" is a meta-game red herring that's doing its job well. I also think the D in aphid stands for Deceive, not Destroy. This allows me to believe that Gemma is on the side of the angels, and for hormonal reasons I'd like to believe she's a good guy.
The infamous phone call could have been Gemma trying to save Mr. Bree. "Are you sure the D in aphid isn't an option?" could have meant "Can't we deceive Bree into thinking he's been killed instead of actually doing it?"