I went into the building and did everything I need to with the single-celled organisms there. Then I went outside to work on the communication arrays. According to the Universal Hint System, I should be able to get the ship to fire phasers for me, but whenever I use the communicator, I just get a pre-canned dialog in which Captain Kirk says we're not ready to beam up yet. McCoy gave me a hint once saying that I should use the ships phasers, but I can't get him to say it again.

Do I have to start the mission over and fix the arrays before I go into the building?

In the middle of the screen with the first antenna is a darker area between the rocks in the background. Scan it with Spocks Tricorder and he should tell you that this would be a good spot for the ship phasers to fire at. Then you should be able call the Enterprise and order a shot from the orbit.

Thanks for the reply!