…It’s tricky: Malfunction negates Keeper abilities, but this “power” is not something on the Enterprise Keeper, it’s described on the Doomsday Machine Creeper, which is not the thing that’s Malfunctioning.
A: The Doomsday Machine is susceptible to starships such as the Enterprise. This is a quality of the Creeper, and not a power of the Enterprise, so whether the Enterprise is Malfunctioning or not is irrelevant, and actually, more thematically accurate if it were!
First of all, we must understand that in Star Trek Fluxx, the Enterprise “stands in for” similar ships like the Constellation (which is technically the ship which destroyed the Doomsday Machine). Any ship could be rigged to explode “in the belly of the beast” as it were, and the non-functionality of the starship sacrificed would not hinder this. In fact, the Constellation was just such a ship: so damaged they couldn’t even steer it from the bridge, it’s warp drive crippled, limping about with only impulse drive.