There are three classes of NPC in the Cypher System: NPCs, NPC Allies, and Followers.
I went in looking for rules to create a "starship crew" for the game, and my first inclination was to give them all a level and potentially a modification based on their specialty. For example, my level 3 ship's doctor would have a modification in medical, allowing them to perform at level 4 in medical tasks.
This was the right call, and it matches the Followers rule on page 233. The Followers' rule says that an NPC Follower can have several modifications equal to their level, so my level 3 doctor could have medical, biology, and diseases as modifications and get another level when dealing with those fields. Doing this makes the NPC Follower-like, but they aren't a Follower unless a character's ability grants the PC one. We cross into creature and NPC design at this point.
Ordinary NPCs just have a level and a modification if you wish. For the most part, they will be a single number for their level. When an ordinary NPC fights another NPC, it is just level versus level, and the higher level is the winner. The rule for this is on page 215.
An NPC Ally, like a wolf pet of a PC, has a level, and their attacks are rolled for by the PC. This rule is on page 222. For the most part, this can be handled as a cooperative action, as outlined on page 226. Note that pets are not necessarily Followers as defined in the rules. Pets do not usually gain modifications unless the pet is obtained through an ability that grants a Follower.
These modifications granted by the Follower rules are essential! The NPC becomes "extra special" and starts getting bonuses in many areas. A follower can even be 'exceptional' and be one level higher than usual (page 233).
Now, how do you roll a leveled NPC attack against another leveled NPC attack? The game says "rolls for them," but how does my level 4 wolf attack a level 3 orc war chief? What is the difficulty number?
For "level versus level" battles, I use the Vehicle Combat system on page 230. Simply compare the numbers; if the attacker is higher, ease the attack by the difference in levels. If the defender is higher, hinder the attack by the difference in levels.
So, with our level 4 wolf versus the 3 orc chieftain, the difference in levels is one. Our wolf is one higher, so we ease one level. So the difficulty of the attack is the orc's level of 3, eased by one level, to a difficulty of 2, a roll of 6 or higher on the d20. What is the damage? A level 4 wolf would do their level as damage, normally, unless the wolf has a modification to damage, which would add one to five.
Followers are notable NPCs granted as allies through character abilities. For the most part, they act just like NPCs in most ways. They can grant PCs assets in various tasks. When the follower is level 3 or higher, they can grant a PC an asset to attack and defense, but only if they have a modification that allows them to do so, such as "assists defense" for a shield bearer. This is all on page 233.
If a Follower attacks another NPC, you have just ruled "level versus level" or handled it like vehicular combat. If you need extra depth and detail, take the time to play it out in wargaming detail; otherwise, use your best judgment and incorporate it into the narrative.
So, for my starship crew, all I need is a list of NPCs and any modifications they have. I won't go whole "Follower level" with any of them unless the PC gains one as a follower; they will all be standard NPCs with a few optional specialties.
The Cypher System makes this easier than any other game. If you are running a large starship crew, a superhero group, or a fantasy guild full of NPCs, no game makes it as easy as this. I remember in Star Frontiers needing a character card for every NPC, or in D&D 4E, having a full character sheet for everyone in the player's guild. It was a massive amount of bookkeeping for no good reason. If you run a guild where PCs take a group of NPCs out for an adventure, only the PC needs a character sheet; everyone else is an NPC with a level and a few modifications. Since a modification can be a power, you can simulate traditional fantasy classes this way easily.
Followers gain special modifications, can assist in attacks or defenses, progress in levels, and can be exceptional because they cost a character pick.
NPCs (and NPC Allies) are mostly the normal "everybody else" in the world, and should not be as powerful or versatile.