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I have been flipping through all the old codexes and a whole bunch of them mention the Nova-Terra Civil war

Can anyone explain this to me? I am unsure what it is about.

There isnt that much to tell on the subject. The Nova Terra Civil War took place when the leaders of the planet Nova Terra seceded from the Imperium and claimed rulership over Segmentum Pacificus. It took several hunderds of years before the Imperium crushed the rebellion. At some point parts of the Adeptus Mechanicus also joined the rebellion causing civil war amongst themselves. The latest Dark Angel codex hints at the possibility of Cypher influencing Nova Terra's secession.

Just goes to show that the Space Marines can't be blamed for all the Imperium's civil wars.

Not even most of them, frankly. Man is weak.