Hi.
Relax. It’s all for fun.
To start, have your PCs all junior officers, Lieutenants and Ensigns aboard a large starship so the big, big decisions are out of their reach. They are Landing Party 3 on the roster, for example.
Preparation for tangents. I prepare alot of NPCs and Supporting characters in advance, by Division, Specialty, and Species. So If I need a Security Officer for the Brig I can use one I just made.
Locations: Players want to wander an open world, so have some premade generic locations and some NPCs to staff it. Bar, Temple, Shops. Make a floor plan so you can keep it straight. What ever you name, then write that directly onto your copy.
Hold back rewards and experience, string it out. Exceptional items require exceptional enemies to counter them. Sort of why these shows keep having to save the entire galaxy in seasons 1,2,3. Players carry the Starfleet issue, not the quantum, wormhole tech powered, ultra fusion phaser with AI targeting assist. If you give something that unbalances your game, take it back. It’s stolen, a stray disruptor beam strikes it, Section 31 has Admiralty orders to confiscate.
Build Missions to hype one Division, give your players a chance to be the hero of the Mission. A Command mission that needs diplomacy. Engineering that solves a village crisis or restores power to an alien sleeper ship, a Security mission that thwarts Orion Pirates smuggling operations, the Medical mission prevent a virus or render aid in a catastrophic natural event.
When you get good at that, combine Command / Security mission to uncover criminals, Security / Engineering mission to infiltrate a pre-warp civ and clean up or recover lost tech or a accidental contamination. A Security / Medical mission to infiltrate a Badlands former Fed Colony to gather evidence of Augment experiments.
Stat out ships, shuttles, and small bases. You will go through those alot.
For practice, have a session zero, had out some pre-gen characters and set up for a few rounds of combat, so you and your players have expectations of how Combat and Skills are run.