Stealth technology has been introduced in conjunction with AWACS vessels during the Main FreeSpace 2 Campaign. The only canon stealth spacecraft are:
A stealth spacecraft is all but invisible to enemy radars and can only be detected via visual contact. This kind of spacecraft are used in reconnaissance missions because their weaponry, armor, and shielding are too poor to survive prolonged battle. The nature of this stealth technology is not explained.
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 hull shape and micro-roughened hull, allow it to evade sensor detection. However, due to an oversight by the GTI, a small modification to standard sensor subsystems nullified the Loki's stealth capabilities.
Some references to the Zeus's supposed stealth capabilities can also be found in ST.
In Operation Templar, a stealth prototype was also under development by the Hammer of Light. However, the prototypes were located and destroyed before they could be produced, supposedly ending the program.