Despite all the base's power being down, Crowbar still enters the meeting room with the its sliding glass doors opening.
It is never made clear how the Shadow Force vehicles and Robot Drones are unaffected by their own EMP weapon.
There is no reason for the Shadow Force to take so many hostages from the power center they've commandeered, unless they anticipate detection and an attempted retaking by Starcom. Moreover, if they're indeed expecting such, they never make it known that they've got those hostages.
It is never explained why, if Cowboy and Crowbar have a shoulder-fired missile launcher with them, they don't simply blow up the power installation...rather than going to all the trouble of sneaking inside. That is, unless they're (somehow) aware of the hostages which the Shadow Force is (presumably) keeping therein.
It is difficult to believe that the Shadow Force would place a single Robot Drone on sentry duty for such an important target as their EMP-emitter...particularly a drone which is easily disabled with one blow from a wrench-wielding Astro-Marine, besides being stupid enough to fall for the "shoelace trick".