I think some other people have noticed this, but there are unused ship abilities called Stealth and Detect Stealth. As far as I know they have not been and will not be used in GC2. You can make a ship part give a ship those abilities but it won't do anything. I am going to lay out a case for how Stealth/Detect Stealth could work.
1. There would be a series of stealth technologies and a series of anti-stealth technologies, each of which unlock ship parts which would give increasingly better stealth/anti-stealth per unit size at increasing cost per part, much like other ship abilities. Starbases (especially military ones) would have modules to detect stealth or enhance the stealth and detection abilities of friendly ships in the area. Presumably, an object as large as a starbase would be impossible (or at least infeasible) to hide with stealth.
2. Here is how it would work in-game:
i. Basically, this is a cloaking device. Ships or stations without anti-stealth cannot detect any stealth ships.
ii. Ships with less than half the anti-stealth number of the ship they are trying to detect cannot detect the ship. Ships with at more than half but less than the anti-stealth number of the ship they are trying to detect suffer a hit percentage penalty in battle. For example, if a ship has a stealth number of 8 an enemy suffers the following effects:
0-3 Cannot detect target
4 Can detect target but cannot attack target
5 Can detect and attack target but can only hit 25% of the time
6 Can detect and attack target but can only hit 50% of the time
7 Can detect and attack target but can only hit 75% of the time
8+ No adverse effects
iii. Ships must decloak in order to attack planets with troops or spores.
iv. Stealth ships that cannot be detected by the enemy at the time of a war declaration are exempt from the United Planets Neutral Ground Law, if such law is in effect.
3. Stealth and anti-stealth would be new abilities, which could be selected in the race abilities screen. I would recommend it taking 10 ability points to get a +1 bonus to stealth or anti-stealth, and being able to get back about 8 points by taking a -1 penalty to stealth or anti-stealth, as this ability is VERY powerful if used properly.
4. This could be required for espionage, along with a spy module, to deliver spies to (or extract spies from) enemy planets. Getting caught in the act of delivering a spy would hurt diplomatic relations, of course. Destroying such a spy ship would not cause a war with the power that sent it unless the party that would have been spied upon wants to go to war over the issue.