Talk about complicated situation, sheesh...
The way i see it, the MC will sadly, eventually have to face the Emperor, if the Compact, it's people that are currently bonded with the Shroud, and most importantly, him, are to live.
If that's the case, then the first thing he must do is make sure everyone is on board with whatever plan he has, that includes making sure everyone is loyal to him, not sure how Timaeus will feel about it, but i suppose you could try to persuade him by allowing him to speak with his Father, try and see if Diplomacy works. Have a feeling Timaeus will need to pull a straight 100 Speech Check: Persuasion + Education History/Culture + Biology (Chemistry and Psychology) all mastered to even keep up with the Emperor, and even then... be Ready to bail him out if things go south.
For the moment, the smart thing to do is:
1. Find an empty planet to settle your people that is to be marked as the capital of the Compact, maybe give it a quirky name like Avalon, that's meant to stand tall as a beacon of Light in an otherwise bleak Galaxy.
2. After settling in and strengthening it properly, draft a Constitution, a set of Core Common Laws that everyone can agree on that are supposed to act as the Foundation/Bedrock upon which the Compact is found on formally. Do also try to create a culture that promotes the support of the Compact, a culture that sees people of all races self-identifying as part of the Compact first and foremost, and secondly as a citizen of their own country/world/race. Emphasis on the Constitution/Shroud as the Core tenent upon which the culture is founded on.
3. Try to find the other planets populated by other people, be they human or xenos.
Take a look at their tech level - which depending on it will make things easier or harder if war is the only choice, culture/history - stance on other governmental entities and biology/psychology.
4. Once done, see if Diplomacy is possible.
I. If they're ORKS then PURGE or/and DEVOUR them.
II. If they were infected by CHAOS then PURGE or/and DEVOUR them.
If there are any packets of untainted people or those whose Souls can still be saved then try and rescue them, do make sure to have to have your Psykers subtly mind check them to see what kind of people they are, and if they're a threat to the Compact. After that, they should be grateful enough to want to join the Compact.
III. If they're just a normal world, then you need to pay attention to their race. If they're Xenos, then it's important to know if their biology/psychology is not too alien from that of a human, if it is, then you have two choices: assimilate through gene modding or exterminatus.
IV. If exterminated then take the planet for the Compact once done.
If assimilated, make sure their biologically/psychologically similar to humans. After that take a look at their culture/history and see their stance on forging an alliance with the Compact. If the current leaders/regime is too oppressive attempt to covertly remove them, and instead prop up new leaders/regimes that are more in tune to what the Compact wants. Then add them to the Compact as well.
In case if they've been genetically modified and they eventually find out then simply explain to them the reason for the gene uplifting has to do with being able to properly empathize with one another. Also make sure to show them the precise documents pertaining to what was changed and why in great detail. Make sure to pay attention to any would be ambitious people that might plan on causing a rift between the gene uplifted race and the Compact for their own selfish means, and excise said tumor before it grows out of control.
If done this way, then before long you should be able to rebuild the Alliance back to its former glory. Especially for when the Compact gets to finally meet the Imperium.
On a side note, you might want to give Timaeus his own Legion, albeit make sure they're all Astartes Primaris + with Apex Level Psykers instead of just normal Astartes as well as a WAAAGHHH/SHROUDED Primarch field. Should be possible by shortening the research time using the Shroud as a conduit to analyze his biological makeup to create a proper gene seed.
Other than that, maybe the MC should use their knowledge to get access to some Necron/Old One tech early on to combat the Imperium. Also get in contact with packets of the of the remainder of the Eldar Race that are still alive, maybe persuade them to join the Compact by having the Shroud clean some of the planets that haven't been pulled in the Warp Storm and/or find the secret to making those Soulstones and giving it to them.
And lastly, my reason for being wary of the Emperor is because of this:
Edit: Also considering that in this timeline the Emperor's kicking it up all the way to eleven because of the Shroud's Presence might make the Imperium stronger than it was in canon, possibly even DAOT level depending on how much of a threat he sees the MC's shadow.
As for the Heresy, it's more likely that it will be called the Timaeus Heresy, with potential rebels such as Guillman, Sanguinus, Angron, Magnus, Konrad Curze joining, with the Shroud capable of fixing Sanguinus's Red Thirst/Black Rage, fix Angron's Fried Brain, fix Magnus's Unstable Legion, remove Konrad's nightmares/fatebound curse etc. Now that'll be weird...
The way i see it, the MC will sadly, eventually have to face the Emperor, if the Compact, it's people that are currently bonded with the Shroud, and most importantly, him, are to live.
If that's the case, then the first thing he must do is make sure everyone is on board with whatever plan he has, that includes making sure everyone is loyal to him, not sure how Timaeus will feel about it, but i suppose you could try to persuade him by allowing him to speak with his Father, try and see if Diplomacy works. Have a feeling Timaeus will need to pull a straight 100 Speech Check: Persuasion + Education History/Culture + Biology (Chemistry and Psychology) all mastered to even keep up with the Emperor, and even then... be Ready to bail him out if things go south.
For the moment, the smart thing to do is:
1. Find an empty planet to settle your people that is to be marked as the capital of the Compact, maybe give it a quirky name like Avalon, that's meant to stand tall as a beacon of Light in an otherwise bleak Galaxy.
2. After settling in and strengthening it properly, draft a Constitution, a set of Core Common Laws that everyone can agree on that are supposed to act as the Foundation/Bedrock upon which the Compact is found on formally. Do also try to create a culture that promotes the support of the Compact, a culture that sees people of all races self-identifying as part of the Compact first and foremost, and secondly as a citizen of their own country/world/race. Emphasis on the Constitution/Shroud as the Core tenent upon which the culture is founded on.
3. Try to find the other planets populated by other people, be they human or xenos.
Take a look at their tech level - which depending on it will make things easier or harder if war is the only choice, culture/history - stance on other governmental entities and biology/psychology.
4. Once done, see if Diplomacy is possible.
I. If they're ORKS then PURGE or/and DEVOUR them.
II. If they were infected by CHAOS then PURGE or/and DEVOUR them.
If there are any packets of untainted people or those whose Souls can still be saved then try and rescue them, do make sure to have to have your Psykers subtly mind check them to see what kind of people they are, and if they're a threat to the Compact. After that, they should be grateful enough to want to join the Compact.
III. If they're just a normal world, then you need to pay attention to their race. If they're Xenos, then it's important to know if their biology/psychology is not too alien from that of a human, if it is, then you have two choices: assimilate through gene modding or exterminatus.
IV. If exterminated then take the planet for the Compact once done.
If assimilated, make sure their biologically/psychologically similar to humans. After that take a look at their culture/history and see their stance on forging an alliance with the Compact. If the current leaders/regime is too oppressive attempt to covertly remove them, and instead prop up new leaders/regimes that are more in tune to what the Compact wants. Then add them to the Compact as well.
In case if they've been genetically modified and they eventually find out then simply explain to them the reason for the gene uplifting has to do with being able to properly empathize with one another. Also make sure to show them the precise documents pertaining to what was changed and why in great detail. Make sure to pay attention to any would be ambitious people that might plan on causing a rift between the gene uplifted race and the Compact for their own selfish means, and excise said tumor before it grows out of control.
If done this way, then before long you should be able to rebuild the Alliance back to its former glory. Especially for when the Compact gets to finally meet the Imperium.
On a side note, you might want to give Timaeus his own Legion, albeit make sure they're all Astartes Primaris + with Apex Level Psykers instead of just normal Astartes as well as a WAAAGHHH/SHROUDED Primarch field. Should be possible by shortening the research time using the Shroud as a conduit to analyze his biological makeup to create a proper gene seed.
Other than that, maybe the MC should use their knowledge to get access to some Necron/Old One tech early on to combat the Imperium. Also get in contact with packets of the of the remainder of the Eldar Race that are still alive, maybe persuade them to join the Compact by having the Shroud clean some of the planets that haven't been pulled in the Warp Storm and/or find the secret to making those Soulstones and giving it to them.
And lastly, my reason for being wary of the Emperor is because of this:
Edit: Also considering that in this timeline the Emperor's kicking it up all the way to eleven because of the Shroud's Presence might make the Imperium stronger than it was in canon, possibly even DAOT level depending on how much of a threat he sees the MC's shadow.
As for the Heresy, it's more likely that it will be called the Timaeus Heresy, with potential rebels such as Guillman, Sanguinus, Angron, Magnus, Konrad Curze joining, with the Shroud capable of fixing Sanguinus's Red Thirst/Black Rage, fix Angron's Fried Brain, fix Magnus's Unstable Legion, remove Konrad's nightmares/fatebound curse etc. Now that'll be weird...
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