Okay, think I have an official game plan for 40k, using just Fine Structure and Genius the Transgression as a base.
1. Find a region of space that was not interacted with at all since the early period of the Dark Age of Technology. This can be done using Genius Truth Machines, both for narrowing possible locations and then getting confirmation that it won't be interacted with after we set up shop.
2. Time travel back to right after the beginning of DAoT and begin setting up shop, establishing a massive base of operations to produce things for later steps. Materials can be sourced via Fine Structure science and then produced en masse via Genius factories, optimizing them toward speed.
3. Slowly and discretely expand a teleportation network through the galaxy, excluding the future Warp-controlled area. The one flaw with Genius FTL compared to Warp Travel is that it is far slower on average, so to counter any issues, we have to use keyed Teleportation Gates instead. We will also make sure these can't be found easily via Genius Truth Machines. Use these gates to Von Neumann additional production sites so we don't have a critical weakness.
4. During this period, create a massive amount of arms and material with a variety of purposes, including ship-to-ship, orbital bombardment, anti-infantry, and anti-genetic weaponry, as well as intersystem weaponry as a special surprise we will use later.
5. Once all automation for the above is set up, take a pit stop in the DAoT to destroy what will become the source of all scrapcode. While there is already a Genius defense to counter scrapcode (Protasia can explicitly protect against metanormal hacking), it's better to destroy it and make it a non-issue than work to prevent it later.
6. Skipping ahead to the Imperial Crusade, it's time to start kicking ass. Using the anti-genetic weaponry, key it to Orcs and begin exterminating them wholesale, prioritizing higher, more organized units. This will likely get the Orcs to begin scaling up, but with our buildup, we can destroy them before they get to our level.
7. At the same time, impede the Imperial Crusade and deal with any problematic Xenos and Human factions in order to create a formal united without having humanity descend into an authoritarian military state. Deal with minor Chaos cults based on the weight of their actions and whether reform is possible.
8. Begin using Intersystem weaponry to bombard any Chaos-controlled planets in the Eye of Terror. This won't stop Chaos, but it will prevent them from responding.
9. Begin using massive Blackstone structures to begin pushing back the Eye of Terror, hopefully to the point of banishing it to a very limited number of systems. If possible, start killing Chaos Gods at this point to hopefully guarantee that this shit doesn't get worse.
10. Now that all the things making the Galaxy worse are dealt with, improve conditions to make it better.
11. Easily curbstomp the Tyranids with 25k years of preparation. Win.