Threats
Threat Name: A name and general description of the threat the PCs face.
Initiative: The statistic and appropriate modifier the threat uses to determine its initiative.
Skills: A list of skills relevant to the threat in an encounter. This should be filled in only if the threat has some means of using the skill or the skill is relevant to an ability the PCs might possess in the encounter.
AC: The Armor Class of the threat, if any. Some threats might be intangible (such as a computer virus affecting the PCs' starship during the scene) or too large in scope to attack (like an asteroid field) and won't require an AC entry.
Saving Throws: The relevant saving throws of the threat. In most cases, this indicates a Fortitude and Reflex save, but sometimes (such as with a living creature) a Will save might be necessary.
Hit Points & Shields: The Hit Points and Shields of the threat when relevant. Generally, a threat should have no higher than moderate Hit Points and only have Shields equal to the minimum resistance of the scene's level, if shields are appropriate on the threat.
Threat Routine: Like a complex hazard, each threat has a routine it performs on its turn in the initiative order. This routine lists the specific actions the threat takes during its initiative as well as relevant rules.
Designing Threats
Complications: Some threats should exist to complicate the PCs' actions. In a scene where the PCs act to obtain Victory Points, then consider having a complication that exists to stymie their efforts by imposing a skill penalty unless a crew member acts to negate the complicating hazard. In combats, this complication might be a nebula that scatters targeting and imposes a flat check on attacks akin to concealment, unless a crew member acts to overcome the effect. This works best with environmental effects and provides a good way for less direct roles, like magic and science officers, to interact with the encounter.
Indiscriminate Threats: One way to add an additional threat without breaking the overall balance of the encounter is to include a threat that targets everyone in the encounter indiscriminately. An example might be a magical effect that blasts the area with energy and blinds sensors (possibly requiring a crew action to counter) or an environmental effect that damages every side in a conflict. Having a hazard-like threat within the encounter that deals damage with a basic saving throw and affects the PCs and other present threats generally balances a combat-focused encounter but could have more ramifications in a timed event, as extra damage means the PCs can't remain operational for as long.
Multiple Starship Threats: Battling against a squadron of enemy fighters is an iconic scene, but if you include multiple enemy starship threats, the PCs can quickly find themselves overwhelmed. Instead, you might consider looking at the appropriate Hit Points and damage of one threat, then dividing it into groups. An appropriate 4th-level threat in a cinematic starship scene could have a moderate Hit Points of 60 (as per the Hit Points table in Building Creatures), which you could break down into groups of 15, giving you a total of four fighters. The damage of a moderate 4th-level threat is 2d6+5 damage per round, so you might consider having each fighter deal 1d6+3 damage with their attacks, meaning if each enemy fighter hits the PCs, they take more damage than moderate; however, the PCs compensate by being able to remove smaller threats at a faster rate.