I'm thinking sabotage. Like sabotage probes that allows you to disrupt hinder or prevent action with certain buildings using expensive EM probes. The counter to it would be EM lasers that would be good against the probes (Only thing that can detect the probes) and light defense against other things IE Light fighters...ect. the requirements would be a new research called Stealth ops to level 1 stealth ops would cost 1.5m metal and 1m crystal. After that the probes are 60k metal and 30k crystal with 15k det. (The more probes the more likely to be successful). The attack would work like a missile attack or an Espionage.

New ship, defense, and research for one idea? Sounds like a big order.
What kind of preventative actions? Increased research time? Lowered energy production?
Specs for the defense? Cost and stats?
Requirements for Stealth? Is there a maximum optimal level? Cost increase?

A lot of questions to answer.