Let's say a planetary cartographer is going over the maps of the known worlds.  Just check each map for accuracy and matches the data in their computers.  It just so happen he does three maps in a row and discovers that on each of these planets there is the exact same island.   All three islands are the same diameter and made from granite, there is a central lake and it is fed by four large natural tunnels.  General speaking the islands general appearance is that of a mesa.   He notes his findings and passes them up the change of command.

The Interstellar Survey Team (IST) would most likely put such a find on the back burner because it's not a clear indication of intelligent life.  There is also the distance between planets which seems to indicate that this is a random geological event.  This would delay the discovery of our ancient alien by several years.  Nor could you say without definite proof that they were natural formations.

When they finally get around to sending a Geological team to these three worlds, they realize there might be something to the cartographer suspicions. The tunnel ordinations are magnetic north to south east to west.  This allows the Geologist to date them at approximately 20,000 years before the present civilization.  There is also some evidence that something had cut the tunnels through the granite.

They report these findings and a second planetary survey is conducted on all three planets.   The information indicates the following:  Atmosphere is basically the same.  The planets are poor in mineral resources but great for farming which is what they are used for at present.  Animal never evolved beyond small primates, while the plant life consists of many grasses and small brush.   Conclusion:  The planets had either been stripped or terraformed.

There would be much debate about these planets on all sorts of scientific levels adding to the confusion, popular myth, and conspiracy theorist.   Quietly the IST begins investigating the possibility of an ancient alien race.  Occasionally some crackpot writes a tell all book about the IST activities and cover-ups leading everyone in the wrong direction and creating a larger than life mythos surround the actual finding from the original report.  So when the actual discovery of an alien artifact is discovered, the general population blows it off as some crackpot seeking fifteen minutes of fame.

The ship that is discovered is spherical in design and mistaken as a planetoid circling within a gas giant's rings. The centuries have not been kind making the ship appear to have suffered many small impacts and covered in a dirty layer of ice and dust.  It's only after the mining company does an exploratory shaft do they discover that it’s a ship.  There is some delay in reporting the find adding more intrigue to the story I have thus woven.

When the IST finally get their hands on the ship several things become clear.   The large crater at the South Pole match the diameter of the islands discovered and is a part of the drive system.  The smaller impact craters are from weapons fire and the ship was abandon since no bodies were found on the ship.

You can take it from here...