I'll go ahead and give an example of what I have in mind... it's just one example of an exploration / combat site.
You find a wormhole in space and jump through it. On the other side you are into unknown space, a quadrant far far away...
You look around the nav computer and spot a star nearby... Jump there and start to explore the planets / moons. At a moon you spot a derelict station in orbit... The station is just a mere satellite outpost, but upon close inspection, you find a sealed capsule with writing on it... removing the capsule from it's spot triggers a self-destruct mechanism on the satellite.
After some debate among your scientists, they are pretty sure the devise is a key/tracer to an alien research facility.
You now have two choices:
1.) Return to Earth and sell the capsule for nice solars
2.) Follow the trail to the secret alien installation
The facility is in deep space so you proceed to the indicated coordinates. When you get there, you have to use the capsule to reveal a cloaked area of space. Upon revealing the cloaked bubble, you notice the facility is actually the size of a small moon, in deep space. Robotic defenses all around... You attack the facility and finally manage to get to it's cargo bay to find inside... an alien death ray weapon, that bypasses shields / armor and does 1000 damage to crew directly...
Your scientists tell you that it seems the site was a top secret alien facility... that maybe the aliens are nowhere to be found because they used that weapon and destroyed themselves... or maybe not