Stealth technology was introduced in conjunction with AWACS vessels during the Main FreeSpace 2 Campaign. The only canon stealth spacecraft are the GTF Pegasus and the GVF Ptah.
A stealth spacecraft is all but invisible to enemy radar and sensors, and can only be detected via visual contact. This kind of spacecraft is exclusively used in reconnaissance missions because their weaponry, armor, and shielding are incapable of surviving the heat of prolonged battle. The actual nature of this stealth technology is not explained in detail, however masking material, hull shape and blending technology are mentioned.
In Silent Threat, the Loki-class recon fighter was also referred to as possessing "stealth technology", although its capabilities were greatly inferior to those of more advanced craft such as those mentioned above. The Loki's shielded exhaust and reactor chambers, as well as its shape and micro-roughened hull, allow it to evade sensor detection, though it remains visible on radar. Due to an oversight by the GTI, a small modification to standard sensor arrays nullified the Loki's stealth capabilities.
Some references to the Zeus's supposed stealth capabilities can also be found in Silent Threat.
During Operation Templar, a stealth prototype was also under development by the Hammer of Light. However, the prototypes were located and destroyed by GTVA forces before they could be produced, supposedly ending the program.