I've been working on my Apotheosis Drive X setting. This is in preparation for the possibility the Kickstarter funds high enough for my setting to be "unlocked". It's also because I've become invested in it to the degree that I want to see it completed regardless of whether it is included in the anthology or not. However, I'm facing a challenge I willingly took on when I envisioned it: scope. The "bad guys", the ships, the amount of energy being thrown around, and the spans of time involved are enormous. It gets extremely difficult to relate to in any meaningful way.
Some games have tackled scales this large. One of them was Dream Pod 9's Core Command, and its solution was simply scaling things up. A starship that could be any "normal" scaled ship in another setting is just stated as being 100km long. Personal weapons do insane amounts of damage and can blow up ships, ships can blow up planets, etc., etc. At first I thought something like this could work, especially with the Fate Fractal. Create everything as a character and then apply scaling. In this way, everything from solar system-spanning battles down to mecha-on-mecha action could take place.
This approach presents a couple of problems. First, the relative scales make these elements seem less epic. At the same time, the larger scales become nearly as meaningless as no scale at all once they go beyond "system" to "galaxy" or larger. Second, scaling down the obstacles still doesn't create a sense of overall accomplishment. A battle that saves an entire solar system and millions of lives is just one of hundreds of billions of battles that would need to be won. All we've done is trade one incomprehensible situation for another.
I'm leaning toward a handful of related approaches. Two of them are inspired by posts by Michael Moceri on the Fate Core Community. First, instead of having pieces of the Engine (the universe-spanning threat in the setting) at different scales it is simply an omnipresent threat. It will have an Aspect or two that can be invoked or compelled anywhere at any time, and a Skill that likewise can be used to create obstacles, advantages or attacks relevant to its nature. Second is the idea of having a campaign stress track of sorts. This tracks the changes to the nature of the universe as the Engine wins or loses ground. As the players succeed or fail at trying to defeat the Engine, the stress track moves forward or backward. At specific points, campaign aspects can change, increase or decrease in scope, etc.
Of course, this doesn't change the other elephant in the room: a story arc representing only a relatively small slice of time can't result in impactful changes. These are events that unfold over tens of thousands, hundreds of thousands or even millions of years. None of the original characters will be around to see the end. Luckily I think I might have some solutions that will satisfy conveying the impression of the vastness in scope of humanity's struggle.
The first solution is to make the arcs within the game take place during different epochs. Each one focuses on pivotal events in humanity's struggle against the Engine, starting with the discovery of the mecha (called Jotun). In this way, the story can jump thousands of years or more. The events of the previous arc change the atmosphere, tone and specifics of the current one. Arkships change, societies change, galaxy-wide calamities occur. If I posit that the Jotun are pretty much "immortal", individual Jotun could be a link between these arcs. The pilots change, but the mecha continue to grow and get upgraded.
The second solution takes this a step further and draws down on some hard science. Because for all intents and purposes, FTL travel is time travel. Even if space folds incorporate a special frame of reference to work, relativity and causality are still considerations because not everyone is in the same frame of reference. This means that the player characters, along with their ship, can fold through the entirety of the multi-million year war against the Engine. They can observe the effects of battles that haven't happened yet, and participate in events that from their perspective already have. Distant descendants may actually originate from the character's past. With this setup, chronology of events has nothing to do with when they took place in regard to the greater universe, but the order they took place from the character's point of view.
That, my friends, is thinking big.