While it is true the Imperium is up there in the evil department, they aren't the big bad because in the long run they are doomed. If we were using the evil argument, the Deldar and Eldar win by far. Going by the strength argument they also lose. They can't fight any of the four strongest factions, and were destroying themselves anyways. Actually, when you think about it they are kind of like a bigger, more popular Tau. They think they are the good guys, use up way to much screen time, and won't make it to the final battle. Anyways, when I speak of the big 4, I mean the only factions with a chance of winning. Those would be the Necrons, Tyranids, Chaos, and Orks. C'tan are not included as they are currently not a faction, though if the Dragon of Mars awakens they will be. The Orks are a maybe/wildcard faction. If they can get their act together and go Full Krork, they can win. This could be done the hard way pr by finding Qah, the last Old One. This is a long shot though, and they are hard countered by the Tyranids. No matter what, as they are they cannot win against them. If they go full Krork maybe. They have a good chance against the Necrons if they Go Krork or even now maybe, and a slightly less than 50/50 against chaos. The other three are basically the Triumvirate of you best bets for winning 40k. Chaos is in the worst position as the Tyranids laugh at their coms, disable their FTL, crush them in melee and Blot out the warp. They can permakill daemons via malantai derivatives, and are basically Chaos's hard counter. Necrons on the Other hand simply annihilate chaos in space and on the ground, and are in an incredibly defensibly stable position, more so once all their anti warp tech is up. If they make enough pylons, and chaos cant really cant really contest those worlds because they just flat out lose in space, than it is GG chaos. Chaos has magic and Daemons going for it, but both other factions can counter it. That leaves the Two strongest factions, Tyrant Beasts vs Mirror Devils. They are the two most likely to win 40k. On one hand, the nids have an absolutely horrifying numerical advantage, and an unheard of level of cohesion. Their numbers are unknown, but they range from 12-1000's of galaxies worth of nids. Or, in other words enough nids to occupy The City. They fleets are similar, with the as the splinter fleet of the Baal tendril of Leviathan over Cryptus had Millions of ships. To put that into perspective, using this logic " The FFG books indicate the average sector caps off around 200 worlds, with a median of about a hundred; with a fleet of 50 to 75 ships of the line and 2-3 times or more their number in escorts, probably not more than 6-fold. A "million worlds" with an average sector size of 120 worlds is about 8300 sectors and 400,000 to 650,000 ships of the line; with maybe 2 million escorts, so 3-5 million combat ships is probably a reasonable approximation not based on outliers." the imperials have 3-5 million total warships (not counting fighters), so a fraction of a fraction of a scout fleet has either equal or more ships than the entire Imperial Navy. They can rapidly adapt to Necron tactics and weapons, and can see everything any of them can see. They also possess psykers, and will have undoubtedly gained obscene amounts of strength from the Ork, Hrud, Rakgol and Kroot genomes by that point. They have no worlds or supply lines to attack, and are able liquidate and mobilize their entire military without having to leave any behind or deploy a rearguard. They also recycle their commanders like the Swarmlord and Dagon Overlord, granting them millions of lives and years of experience. Additionally, they can rapidly switch tactics due to their ability to tailor they troops even while they are being deployed. On the other hands, the Necrons are terrifying. They have a similar (but lesser) coordination, but much better logistics via literal teleporting and fleets that can cross the galaxy before the first spores even start falling. They commanders are even better and they and every other soldier are veterans of the War in Heaven, the first great war all other wars came from and pale in comparison to. They are all very skilled combatants and will be fighting from a fortified defensive position and have the home ground advantage. They can move around their worlds at will and have uncountable and terrible superweapons that make sanity weep, like the World that Rewrites History, or the Celestial Orrery. They also possess Daemonworld like creations, such as said History Planet and Moebius. Their navy is this best in this universe and many others bar none, and can be rapidly produced via the powerful Necron Industrial Base. Said Navy held off the above several million strong fleet almost evenly when it was just the navy of a single tombworld. This navy can also pick the time and place of engagements, and pick off isolated Tyranid fleets and leave due to the relatively slow speed of the Nids, and can concentrate the full might of the navy very easily. They have more worlds than the Imperium (several vs a singular million) and do not flee or fear when bereft of leadership like the nids do. They can permanently destroy biomass with all weapons, and reincarnate infinitely making it so the Tyranids take permanent casualties while they do not. Furthermore, the nids have no way to permakill Necrons, which will invalidate some of their units like lictors as the Lord can arrive back seconds later, while synapse creatures have no such defense. Additionally, they have horrifying individuals in their ranks such as Szarekh, Godslayer Maktlan, Planet Buster and Godslayer Ahmontekh, and I scare flayed ones Xunbakyr. They also possess functioning time travel, and many other powerful advantages like the ability to create entire dimensions (which they use for garbage disposal) and turn things to stone via Crytpeks. And Finally, only they have the experience of fighting and slaying gods, Warp, C'tan, Old One, and Daemon during the war in heaven. Perhaps they could even slay the hive mind. Still, to much is unknown about the full might of either faction, so it could end up as either an Ophilim Kiasoz situation or a New Devourer situation. In other words, it could go either way. Tactics and commanders will be huge here in. Whatever happens, it will be an epic clash that will shake all creation. Well, anyways, to summarize it really depends on what you mean by big bad. If we are referring to evilest race, the Dark Eldar take it. If we are referring to the strongest race, it likely goes to either the Necrons or Tyranids. The C'tan could be both, but their participation is unlikely outside of the Void Dragon awakening or the Outsider showing up. I suppose this is the point where I remind everyone that the Outsider is so bad he scares the Tyranids. They flat out Nope Nope Nope around and away from the Sphere of the Mad One. Or, in other words: TL;DR Dark Eldar>Evil, Necrons/Tyranids>Everyone Else's military unless surprise C'tan interrupt.