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So essentially, here is the background, and why I cannot decide on a few of the details.

This chapter's primary job is to hunt heretics, much like the DA hunts the fallen. They are assassins of sort, The Imperium says, these heretics over here need to be exterminated, go do it. They also believe in the Emperors divinity more than any other chapter.

So this chapter had been sent to wipe out a bunch of the Logicians for heresy etc. etc. They go there, wipe them out, and while they do clean up inside the hide out, they find actual, undeniable proof, of the imperial truth. Files and Videos of the Emperor himself, preaching about his hatred for religion, and how mankind can only survive in the name of science.

Shocked, they immediately take this evidence back to Terra where they can show the Imperium "that they are doing it all wrong and this is not what the Emperor wants". The Imperium says that they will fix it, then sends the chapter out to give aid to imperials besieged by Orks. After the chapter leaves, the Imperium destroys the undeniable evidence, labels the chapter heretics, and send assassins after them trying to wipe them out.

The chapter survives but has no allies, so they look to new technology (more efficeint boltguns, tougher vehicles, genetic experimentation on their gene-seed and physical/mental attributes) to help them survive the onslaught of the chapter from all sides by imperium and xenos alike.

So basically, which codex could possibly represent these guys having slightly better technology than the space marines? Specific chapter tactics (including the FW tactics i.e. red scorpions for FNP tacticals)? I was thinking the CSM codex because the "boons" could represent the new science and I could ignore all the "evil" things in the codex. Plus the prefered enemy against SM could represent more acurate/lethal bolters. But I don't quite like how they have none of the SM new units since this chapter only recently got excommunicated from the imperium so they would have all the hunters/stalkers/centurions etc. etc. and the CSM equipment is intentionally outdated because is is mostly horus heresy era gear.

Also, If the Emporer really is alive and not dead, I see him sending the legion of the damned to help these guys out often. ( Legion checks the emperors tarot to know where to go and more often than not, it leads them to the aid of this chapter which represents the Emperors personal vision on the direction to lead humanity.)

Love the backstory!
I think you should run space marines codex, but have a section of "advanced troops" the mutated, high tech weapons wielding dudes, and use the eldar codex for them using the allies rule and the "counts as" rule.
so one FOC of normal marines, one allied detachment of your sweet, laser-blastin, hover vehicle usein, super marines. (conversions will be necessary to do so, so I'm not sure if you want to, but it would be awesome.)

If you don't want to do that, chaos marine boons, and marks of chaos could be good markers for gene seed manipulation (I.e. Mark of Slaanesh, increased initiative = Higher mobility armor. Mark of Khorne, increased amount of attacks = better weapons, Mark of Nurgle, increased toughness = tougher armor, Mark of Tzeentch, Invulnerable save = force field), and HH era gear works almost Identically to "modern" space marine gear.

Definitely go loyalist, if only for the flexibility allowed. You could ally in Inquisitors with various grenades/guns and psychic powers, and model them up as techmarines.

Definitely go loyalist, if only for the flexibility allowed. You could ally in Inquisitors with various grenades/guns and psychic powers, and model them up as techmarines.

To the OP:

I kind of like the suggestion above for your army. I can see a core force of Iron Hands and an allied set of Inquisitors fitting your fluff really well. The SM book will also give you much more tactical flexibility in the long run.

Your idea is pretty cool btw.

CSM is actually pretty bad for portraying any marine army (including traitors). It lacks any kind of strike force type elements like drop pods, fast transports, infiltrators, scouts, outflankers, hidden models, etc, etc..

It's really really good tho if your chapter is based on slow infantry advance into enemy fire..

Definitely go loyalist and check out the FW chapter tactics.

You could go with Iron Hands as your core chapter and then ally in Tau as well.

Stealth Suits could "count as" upgraded Scouts. Model them like regular scouts with burst cannons and small jump packs.
Broadsides could "count as" upgraded Dreads. Model them as Dreads with the Tau weapons on the arms.
Crisis Suits could "count as" upgraded "Jump Terminators" who trade armor for added mobility. Model them as Termies with Tau weapons on each arm and jump packs.

If you use the Farsight Enclaves book, you can get away with a Crisis Commander as your HQ, 3 man Crisis Suits as your Troops, Stealth Suits as your 1 Elite slot and Broadsides as your 1 Heavy Support Slot.

They would be Battle Brothers.

I do kind of like the tau idea, but at the moment (and probably the far future) only have SM, Ork, and Necron models. My necrons are also only 2 battleboxes and a couple of res orb lords with an extra HQ model.

Jump terminators? Please don't.

scorpio2069 wrote:

The chapter survives but has no allies, so they look to new technology (more efficeint boltguns, tougher vehicles, genetic experimentation on their gene-seed and physical/mental attributes) to help them survive the onslaught of the chapter from all sides by imperium and xenos alike.

Which they get from where? Don't you think that other Renegade Space Marines (Chaos or otherwise) would do the same if they could? Or rather, if superior bolters/vehicles existed (other than master-crafted ones, obviously), why don't other Loyalist Chapters use them (who don't have to go through the trouble of acquiring such material while declared Excommunicate Traitoris)? Where are they learning the skills to augment their gene-seeds in this manner? Apothecaries don't know how to do that sort of thing unless they learn it though experimentation; something that a recently-become-renegade Chapter cannot afford (experiments mean trial and error, and error means the loss of Battle-Brothers that they cannot replace).

I never thought I would see a fan-Chapter who is actually better off while Excommunicate Traitoris without using daemons or magic.

Instead, follow the lines of a similar story; the Minotaurs. If this Chapter has the backing of a non-specified Imperial force (High Lords? Inquisition? Ecclesiarchy?), they could acquire superior gear from there, like the Minotaurs, Grey Knights, and Sisters of Battle. Also, if this Chapter "believe[s] more in the Emperors [sic] divinity than any other chapter", how was this 'proof' they found "undeniable"? You have clearly never debated religion with a religious person before, the kind who will absolutely refuse to accept the fossil record, for example, as legitimate (see Bill O'Reilly; you can't explain that). It would be more apt for one of their number (ideally the Chapter Master) to have received some sort of vision, a spiritual epiphany, hinted-at-but-might-not-be an actual message from the Emperor himself, with it left open as to whether or not the vision came from Chaos. It could have lead them to this proof, and so backed by a spiritual message, they would be inclined to put their faith in it.

scorpio2069 wrote:
aid of this chapter which represents the Emperors personal vision on the direction to lead humanity.

That is too much. Way, way too much. That's crossing well into Chapter of Sues. It's fine for the Chapter to believe that this is their role, but not fine for the omnipresent "author perspective" state it as so. It's also nowhere near as interesting.

In answer to your question; Codex: Grey Knights. Psy-ammo could represent their wealth of special-issue ammunition (so the "better bolters" you wanted), far in excess to that of a normal Chapter. A limited amount of exceptionally powerful/well-equipped Battle-Brothers would fit the theme of, well, the Minotaurs (much more so than the Minotaurs Chapter Tactics, which given their background is more than a little underwhelming). As long as you ran the codex according to your fluff, it would fit.