The last book in the library. [Spoiler for Godblight, Devastation of Baal and Unremembered Empire]

I think most people are underestimating the political fallout of the Imperium Secundus reveal. Guilliman rules the Imperium, yes, but he has plenty of political opposition. He has plenty of enemies in the vast Imperial bureaucracy looking for the smallest chink to exploit, the slightest weakness to leverage, any opportunity to undermine his divinely-inspired authority. They do it because they are human, and humans look out for themselves. Political power is a zero-sum game, and Guilliman has come out of nowhere to seize a total monopoly on it. A great many established interests are necessarily unhappy with that. Primarch or not, humans do not appreciate someone else taking what they see as rightfully theirs.

Calgar had run the theoreticals and practicals of the primarch’s awakening through his head many times before Guilliman had come back to them for real. It was indulgent, wishful thinking – daydreaming, even. But who did not wish for a saviour in times of need? Marneus Calgar, who was looked to as a saviour by billions of people, had needed his own idols to put faith in.

When he had formulated his versions of Guilliman’s miraculous return, as he was sure every Ultramarines Chapter Master since the first had also done, he had not conceived of events playing out as they actually had. He had not foreseen the resistance to the primarch’s rule. He had naively expected a primarch to be able to overcome the stagnation of Imperial government by dint of his presence. The primarch would return, and all men would fall into line, and obey him unquestioningly. They would march together to conquer the galaxy, putting the old enemy to the sword and driving out the xenos.

It had not worked so simply. There was dissension, different interpretations of the primarch’s edicts – sometimes wilful – and there was disbelief and suspicion. Guilliman’s rebirth had caused great rejoicing among the populace, but less so among those leaders who risked losing their influence to his rule. Calgar had relied a great deal on the civilian leaders of Ultramar and beyond. Roboute Guilliman should not need to.

- Dark Imperium

The most blatant example of this is the Hexarchy, an attempted coup at the highest levels of Terran government.

The images came from within the cathedral, seemingly somewhere close to the high altar. The speaker was one I recognised – Irthu Haemotalion, who had once been Master of the Administratum. Next to him were two serving High Lords – Aveliza Drachmar, the Grand Provost Marshal, and Fadix, Grand Master of Assassins. With them stood another deposed High Lord – Baldo Slyst, the former Ecclesiarch.

And there in the background was Moloc, who appeared to be holding a severed head in one hand. From our intelligence briefings, I recognised the bloated features of Fyger Deflaim, the so-called Master of Dreams. His rebellion had been ended almost as soon as it had begun – but then of course he had only been a tool in all this, a means to generate the disorder they needed.

‘Behold, the age of insurrection is over!’ Haemotalion said, addressing the remote oculus with all the polished assurance he had displayed when in office. ‘The heretics are destroyed. The future shall be as in the unchanging past, just as He ordained it, just as the Lex demands.’ He smiled warmly.

‘The Imperium as it was. The Imperium as it must be. Imperium Eterna.’

- The Regent's Shadow

But an open coup is the least of Guilliman's worries. Far more dangerous is simple doubt in his leadership, doubt as to the extent of his ambition, doubt that Guilliman is the selfless saviour he claims to be. Doubt, the dissent it will spawn, and the disunity it will produce. Maldovar Colquan sums it up quite clearly:

‘I have heard and discounted all the arguments of your emissary brethren, Achallor. I know the prevailing opinion among your host, and I disagree. Guilliman is one of the primarchs, the Emperor’s gravest errors! Now he is at the head of legions he himself banned. He is a new warmaster of the Imperium in all but name. I believe completely that the returned Thirteenth thinks himself to be acting in humanity’s best interests, but only because he was made to think that way. He is a pragmatist of the most ruthless sort. When there were twenty, there was a balance built into their combined abilities and propensities. Alone, he is unchecked, so we must be the check.’

‘We do not have the right,’ said Achallor.

‘We have the only right!’ said Colquan. ‘What if he decides that it is in all our best interests that he replaces his father? What if he grows impatient with the machineries of state? He is a creature of logic. One day, he will reach the conclusion that the Imperium might be better if he took it all over himself, and what then? Do we fight him? Do we support him? Do we betray our most sacred trust?’

Achallor had no answer

- Gate of Bones

Guilliman himself is no fool. He knows the potential danger, and takes great pains to avoid any hint of ambition.

It was close to the Throneroom of the Emperor, wellspring of human authority, yet not so close that it appeared he wished to usurp his father. Similarly, although the palace was well equipped for the making of war, including at its heart the Praefectura Astra Superba, one of the finest strategiums on the planet, it was close enough to the great buildings of state to show he was not blinded to the needs of civilian rule.

- Avenging Son

It was no accident that Fabian was barred from the Library of Ptolemy.

Guilliman made a reasonable face, conceding the point. ‘I stand by my actions. One day those doors will be unbarred. What I did there was symbolic. Who even in my own realm read and understood what the library contained? I sealed the doors not against the truth, but against the superstition that has taken truth’s place.’

Guilliman did not lie often but he did then. There was one book in the Library of Ptolemy that told a history he would rather no one read. He could not afford the shadow of the Imperium Secundus to hang over his latest ventures.

- Dark Imperium

Guilliman knows that the very concept of Imperium Secundus is dangerous, because it is the perfect exhibition of his ambition to rule an empire in his own right. To usurp his father. It matters not at all that he had only the best of intentions, that he did not know Terra still stood, that his brothers agreed with him. Those are subtleties lost to 10,000 years of dusty history, and easily glossed over during the big reveal. What matters is that he founded his own empire then, and he leads an empire now–allegedly, in his father's name. What happens when the truth emerges? Because it is, in fact, the truth. Imperium Secundus did exist. Does Guilliman stand up and deny every last detail? Denounce Fabian as a liar and heretic? Or does he say "Yes, but...." and watch his political enemies leap to take advantage?

‘This is Fabian Guelphrain. He is one of the primarch’s most senior ferreters of facts. He is a poker-about-in-the-dust. A hoarder of forgotten dates. He is supposed to construct true histories. Remember that detail. In the book, which I led him to, is the only account of an empire deliberately unremembered. I thought it time to remind everyone about it, and the true scale of the oh-so-perfect Roboute Guilliman’s ambitions. What this Fabian reads in there will infect him like a disease, he will not be able to divest himself of the knowledge. From this point on, he will never be free of doubt – it will fester, and that doubt will shake an empire.’

He chuckled, and stroked the tentacles of his left arm with his right. ‘The rot is setting in, like a crack that lets in moisture or bad air, and with it comes the burgeoning of new life. An idea is as dangerous as the most potent virus.’

- Godblight

/r/40kLore Thread