Social Orientation, motives and agendas. Some Aliens are more friendly then others.
It could be there exists in the Cosmos a tacit agreement of sorts to allow developing planetary civilizations an opportunity to evolve without outside interference. If you follow this idea the litmus test could be the ability to break free from gravitational restraints and succeed in achieving an orbital space presence.
If this is the rule such an overarching principle has been loosely followed in our distant past. Archeological evidence shows skulls, artifacts and construction techniques suggesting that our ancestors were visited and interacted with Alien visitors. Most of this visitation appears to have taken place before the "Flood" where a catastrophic event shifted the earth's axis and plunged Antartica into a deep freeze. If an asteroid can be used to expunge a civilization how hard would that be for a hostile alien presence to make that happen?
On Mars is evidence of a similar catastrophic event. The Asteroids are claimed by some to be the remains of an exploded planet. If some of this is true the question arises whether this was the result of natural forces or intelligent intervention. If our early contacts with the Ebans revealed that these types of cataclysmic events were the result of Alien intervention, then it is easy to understand the need for secrecy and due diligence to develop technologies for our planetary defenses.
The Ebans referred to an Intergalactic war lasting about 100 Earth years. In this war particle beam weapons were used by the combatants and continued until the Eban' s won. They warned about the hostility of several other Alien races. (181-182)
This could explain our governments near paranoia regarding UFOs. If they take an alien threat seriously the cover-up begins to make some sense.