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When thinking about the story of a videogame it is important to first think about how important the story really is to your audience. Sure, a better story will in general be better, but if it's taking too much time or it's feeling strange because you are not a goof story writer it might just distract from the game. A lot of this depends on your genre and in your specific case that means that many fans will be satisfied with a simple setup similar to the following: 

- Who is your character and why are they in the position they are in? 
  - Who was your character in the past? Did your character go through military training and is now simply at the next step of the career ladder? Did some magical coincidence teleport your average-Joe to a magical world where he is thought to be the great saviour? 
  - What happened that made their position necessary? Did some new enemies appear and your character has just what it takes to combat them? Was everyone else killed and people were just desperate for someone to try their luck?
  - What does your character want to do? Is it their dream position? Is it just a means to end the war so they and their family can live in peace again?
- Who is the enemy? 
  - Are there many enemy factions? How do they interact? Are there alliances? Is there only one left and humanity is trying to finally stop them? 
  - Is there one person behind the curtains that needs to be stopped? Why does the person do this? Or is there some sort of court that controls the enemies? 
- Where is the enemy?
  - Where is your starting position in relation to the final enemy? At the outskirts of some region? A small part of the greater enemy territory? 

By answering these questions you can learn a lot about what you have to show to your players through story means. Often there will be advisors, friends and family that interact with your character to explain what is happening in the and how everything works. For example if your character has trained all their life for their position they might have a devouted follower that helps your player take the first steps. If, on the other hand, your character is new to everything happening to them the advisor will explain the rules of the world and why things are happening. 

Answering who the enemy is will give you a clear goal to communicate to the player, which is important so that they will have a greater sense of their position in the game. The game genre you describe is all about crushing your enemies, so having a clear image of the enemy will make it easy to see the goal and interpret what is happening through that lens. 

Answering where the player character is physically located will often help you to understand why there are certain enemies. If you are in the outskirts of some middle-age type empire you will likely only have contact with small standard troops in the beginning and slowly get to the stronger forces. Starting in a lab in the heart of the enemy territory will mean that your player will have contact with enemy technology fast. It's important to have these things in mind as many games in the genre introduce different mechanics and enemy preferences in regards to tactics and equipment throughout different stages of the game. 

For a story you need:

- a starting point
- a goal
- a few important key points in between, for example to show your character growing mentally 
- a couple more or less points between the key points. 

Going from the big picture of "You are a general and that's the enemy" towards a more fine-grained "And to defeat the enemy general you need to kill all three enemy advisors" will lead you to the really fine-grained "And to kill the first of these three you need to infiltrate his laboratory by sending in small elite troops", which is what you want for mission objectives.