Let us first assume there are no witnesses - it is fast. All persons and devices capable of offering contemporaneous data are destroyed. Otherwise there will be some dude who says "Yeh! I was back in the shed there doing stuff, and then here's Villena with a bigass gravity bomb and then he started swinging it around and yelling and then whoa!"
Let us assume also that whatever happens takes all present by surprise to the degree that the dude in the shed cannot send a message about what is going down before he is blown up.
So: your investigators are late to the scene, arriving after transmissions stop. In essence they are a detective, searching the rubble for clues. How to cover up an crime? I can think of 3 ways.
The first: human activities at the base lead to destruction. A warp core breach from mechanical failure. Maybe researches going on at the station go out of control. Maybe they have made a secret discover of some alien item (which you have faked slightly in advance, using coded transmission) which turns out to be bad. I keep waiting for news of the immense explosion at the North Korean nuclear facility, presumably because they did not know what they were doing. You could plant items in the debris field to lend credence to this scheme. You could fake transmission from the base (after it is gone) - distress calls, the dude in the shed (the fake dude in the shed) reporting what is happening - etc.
The other method is a second slower and more methodical destruction greater than the first, to wipe out all evidence. Perhaps something you can engineer but is too slow for the element of surprise - like the giant asteroid. One of my favorite Stargate episodes is where Carter uses a black hole and a star gate to trigger a star into a nova. If the space station is dead and you can use your mega weapons to get the star to go nova that could sufficiently alter the crime scene so as to make your prior strike difficult to detect. The giant asteroid mass could sweep through afterwards and carry everything out of the way. If you have FTL tech maybe you could open a wormhole to move everything to some distant locale - sweeping it under the rug so to speak. If you have antimatter you could spray tiny bits into the debris field until everything had reacted away.
Finally you could frame some other intelligent agent. Maybe a mutinous or mentally ill sailor sets off bombs. Framing the Indians was always a good strategy, Boston Tea Party style & if there are locals you could pin it on them. This would work best if it were someone plausible, like blaming Saddam for 911. Or something little known, like obscure space monsters.