If rolling dice is that important to you, there are rules for GM rolls on page 18 in the GM's book.
On the other hand, here's how I see the way it should work (without dice):
As the GM, you decide the difficulty and the players will attempt to Strike (melee, ranged, or other) or Dodge (athletics in close combat). If they have more results than the difficulty then they succeed.
The difficulty that the GM decides is based on the situation (unstable ground), the player's actions (how difficult the action itself is) and NPC skills or powers (+2 athletics, for example, means that the player needs 2 more successes to hit in melee).
The solution to the NPCs attack the PCs problem goes down to two things:
1) Player reaction- initiative is considered "real time" if the GM gives the player the chance to react to an action, and the player doesn't react, he's hit. If he plays a reaction card or says what he does then he gets a chance to survive.
2) Athletics as a defensive skill- in melee combat you can use athletics to Dodge (the player rolls Dodge to the NPC attack- if the GM allows him.)
For a better understanding about the result of NPC actions, I'd suggest reading pages 14-20 in the GM's book.
(In summary: the idea is that the players are in control of their actions and rolling dice puts them in the spotlight. If the GM is attempting to harm the PCs they get a chance to react (as I've said before about initiative).)
The pirate question at the beginning as an example:
GM decides that the difficulty is just 1 success.
Tommy attempts to strike the pirate with the mop, he rolls and gets 2 success and a computer.
The GM decides it would be funny that Tommy strikes the pirate and the (jam filled) mop sticks to his face (Tommy looses his grip of the mop.) The pirate, turns to the captain and shouts for help. The GM says that it is an attack on Tommy, (the mop swings at his face). Tommy can either duck with an athletics roll or use the "wrong target" reaction card (and the pirate would hit the captain instead). Tommy takes to long to decide and is struck in the face and falls off the boat.