Alien space craft in our airspace, now what?

Not the OP, but SETI unsurprisingly has a number of protocols for releasing a positive result. Though some of those at the organization suspect that journalists would preempt them in practice.

Guidelines:
http://www.seti.org/Page.aspx?pid=780

Declaration of Principles:
http://www.seti.org/Page.aspx?pid=680

Call for international treaty:
http://www.coseti.org/setiprot.htm

Somewhat embarrassing conference, whose members have probably thought about the OP:
http://www.contact-conference.org/index.html

What could they do? Some giant spacecraft from another star settles above a city? If we’re visited by anyone that far in advance of us, all we can do is hope they have good intentions. Any military response would be like stone age people throwing rocks at an aircraft carrier.

I am not asking what we could do but what we WOULD do? President gets woken up. SAC bases go on full alert we drop to at least DEFCON 3. We get our top scientist and culture and linguists in. Try to minimize contact without quarine.