I finally realized why the method they used to get out of orbit was so familiar: It was lifted almost directly from "Warp Speed" @ Travis S. Taylor (available on the free Baen CDs). They added the Space Catcher's Mitt, which was a good thing. In Warp Speed the collateral damage was BAD.
Well, not directly, as Eureka used a wormhole jump which took them outside normal space, and not screaming through the atmosphere at FTL speeds.
The communication method from the capsule was the same as in "Executive Decision", although geekified (not Morse Code).
EMP: You'd think they'd be more ready to handle that!