>>114572
Just to be clear, is the question “how would you write a Jumper plausibly interacting with the setting at a scale that doesn’t entirely invalidate it utterly but also doesn’t leave you at it’s nonexistent mercy?” or is it “name some significant examples of OOC that can address the following issues I’ve described”? Because the former is kind of skewed due to increasing variance because of what a Jumper’s capabilities even are on average. So, I’m going to try to address the latter.
>The actual hero
First of all, that’s debatable. The Emperor of Mankind has been both intentionally and unintentionally written as a callous and ruthless petty tyrant-although his at least nominal concern for humanity as a whole has become increasingly prominent. The Third Magic from F/SN would be a massive asset to sustaining him given that canonically it has the potential to transform Nasuverse humans into celestial object-devouring cosmic superpredators (in a setting where many if not all celestial objects contain spirits of godlike power who wield enough energy to generate pocket dimensions in which reality is advantageous for them, hurl continents like pinballs or warp the laws of probability to manifest a future version of the planet). Alternatively, Fixer Beam from SSSS Gridman.
>Abstract, immortal entities
Shamanism. You want high grade shamanism and other high grade spiritual practices such as japanese-style priestesses like the Cetra (now that Aerith has been retconned into having multiversal influence over her planet’s immune system), such as mastery of Warcraft’s Light on par with Aman’thul, Anduin and other champions. Lower your standards for “the most righteous of men” in 40K specifically because long before the Imperium’s stagnation, humanity experienced brutal war. Canonically an extremely harsh regimen of psychic training, indoctrination and occasional ally slaughter-based rituals have rendered the Grey Knights so inured to Chaos that even the INQUISITION assumes them to be incorruptible. It can be done, even in-universe, it just takes effort so great as to be crazy even by Space Marine standards. Alternatively, unlock the power of the Enuncia which the Emperor almost succeeded at. Side effects may include godhood:
https://wh40k.lexicanum.com/wiki/Enuncia
>Infinitely spawning Orcs
The orcs are technically the stunted form of the Krorks, a superweapon species created by the Old Ones. Theoretically sufficiently advanced manipulation of warp energies might be able to “deactivate” them; being one of the Slann from Warhammer Fantasy: Lizardmen might be a good start since they are created in the Old Ones’ image. Alternatively, Metal Storm and Holy Diver from R-Type. Various Imperium forces (such as those led by Ciaphas Cain) regularly fight off greenskin hordes even without a perk for fiat military brute force and implausible pilot protagonism.
>Every faction
Be more ruthless. Alternatively, take perks such as Banishing Evil from Child of Light that let you make things better even with violence or SAVE the World from Undertale to tilt causality in preference of diplomatic outcomes. I would suggest Golden Ending from Dies Irae, but not only am I trying to avoid the out of universe big guns for creativity’s sake but I need to find out more about the sequel to determine the risk of the perk accidentally spawning in rape cults.
>AI can’t be trusted
AI is at risk but it’s unfair to say all AI is compromised, a Dark Age Ai was found to still be loyal to the old Imperium at one point and the Owlcat Rogue Trader culminates in an AI-like entity animated by a C’tan itself remaining loyal. Stellaris has some perks to write and render code that’s utterly inviolable.
>Any meaningful progress
This is why you need abilities such as Pioneer of the Stars from Fate or perks such as Happily Ever After from Fables to make meaningful progress towards stability that can interfere with abstract chaos entities’ subtle but far from all-encompassing machinations (see the cope about Tzeentch’s relationship with Kairos as his repository of knowledge Tzeentch himself finds it hard to process)
>Magic and FTL (Warp) travel
Research inertialess and deterministic FTL, the Necrons have some. Alternatively, research the creation of the comparatively safe Webway. Alternatively alternatively, use Space Bridges from Transformers and use Primus-blessed artifacts to safeguard them.
>Large amounts of time
The Aeon Paragon from Supreme Commander generates arbitrary amount of mundane resources, let alone the Imperium’s corpse-starch shitcakes.
>Game of Thrones tier politics and betrayals
A drastic understatement given the level of civilisational advancement in Westeros. Anyway, this one is by far the easiest to address because many 40K jumps provide perks approximating everyone from the average Inquisitor to a smarter than average Primarch or Custodian to Vect or a C’tan itself which should make you a competitive player. Alternatively, take Irregular’s Rebellion in Ricrod’s Highschool DxD and succeed by being aggressively stupid.