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Imperium tried to assault the Chaos held planet of Dharrovar, and got their asses kicked. Completely wrecked. The armies and ships Chaos is bringing to the table this time completely dwarfs what they used during the 13th Black Crusade.
In a surprising move, the Chaos fleet bypass Vigilus; they don't need or want that planet anymore and move for the galactic south.
Huge naval battle between an Imperial fleet and Chaos erupts, and the Imperium loses again. Chaos now controls most of the Nachmund Gauntlet. So getting to the other side of the Rift here is pretty much closed for the Imperium now. Though Chaos gets delayed long enough conquering worlds for the Imperium to regroup.
The Imperium decides to try hold the line by creating a "Sanctus Wall", a long line of planets with a Shrine World at its heart that will be heavily defended with tons of Imperial forces. To get this ready, they sacrifice a bunch more worlds to slow down the Chaos fleet while their reinforcements arrive. Almost every single Space Marine Chapter is brought in and represented here; the Imperial forces being marshaled here are massive. They have to be, as this might be the biggest force Chaos has assembled since the Horus Heresy. Abaddon has been really busy it seems. And his lieutenant Haarken Worldclaimer has proven himself to be a good commander and worthy of his title.
So big Chaos victories so far, but with a Cadian Gate 2.0 being set-up to maintain the status quo. Can't have Chaos be knocking on Terra's doorstep just yet. There's more models and codexes to sell, after all.

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At this point, Magnus is a being of pure warp energy, but not a deamon prince yet. Tzeentch has given Magnus the rope to hang himself, but doesn't have a claim on his soul yet. Magnus disapproves of both Chaos and the Imperium, seeing both as unworthy of charting humanity's destiny or controlling the galaxy, and after he gets his last shard back, he's planning to kill the Emperor and then kill Horus and lead humanity himself into a new golden age under his rule. He hates how both Big E and Chaos have lied to and manipulated him and he wants to be his own master, and get revenge for Prospero and protect his legion. Magnus is convinced his last shard contain all his goodness, and if he can get it back, he can save himself and find redemption, but its suggested several times that this is Magnus just lying to himself so he doesn't have to face the truth, that no one shard contains more or less good than the other, and Magnus' choices since Prospero cannot be excused by saying he's incomplete.
Magnus and a small group of Thousand Sons slips in through the Emperor's shields through a crack only sorcerers of their level of mastery would notice, and infiltrate the Imperial Palace through the elaborate underground tunnels beneath it.
Magnus bumps into Malcador and another Perpetual friend of Mal's, and after a tense talk begin playing a game of chess. Mal is trying to win Magnus over, admitting that he and Emps made big mistakes, and it looks like he's making some progress before he says the wrong thing and starts setting off Magnus' temper. He then mentions that his last shard is no longer here, beyond his reach. Now pissed off beyond words, without even trying, Magnus effortlessly kills Malcador, frying him with a blast of psychic energy. Mal is dead-dead, beyond the ability of even a Perpetual to regenerate or reincarnate from. He then marches up into the chamber with the Golden Throne to confront his father.
Emps feels Malcador’s death, but when taking about it with one character, he’s indifferent and cold, saying his death doesn’t mean much in the grand scheme of things, and when talking about it with another character cries tears of sadness and regret. With the whole “people experience the Emperor through a biased filter their puny minds can comprehend rather than with the objective truth” thing they got going with Big E, it's unknown how he really feels about Malcador dying. Your interpretation is as good as any other.
In the throne room, Magnus meets an avatar of his father, the one named Revelation, and the two begin talking. The Emperor let that small, subtle crack in his anti-demon shield form because he knew Magnus would find it and he knew Magnus wasn't yet a lost cause, so that they could have a father-son chat. He’s even preventing the Custodes from interfering and interrupting their meeting. Magnus isn't caring very much for his dad's speeches, and easily slays the avatar in one-shot. He sees the true Emperor on the Golden Throne unable to defend himself because he's preoccupied with holding Horus' psychic attacks at bay, maintaining the anti-demon shield around the palace and keeping the Chaos infested Webway Gate shut. Magnus charges up his spear with enough psychic energy to seemingly kill the Emperor where he sits, but finds himself hesitating, unsure, feeling not triumphant but more lost and confused than ever. At this point, Vulkan reveals himself.
Magnus and Vulkan have their brotherly talk, and Emps manages to get a brief window to talk to Magnus directly. He says unlike his brothers, Magnus's fate is still undecided, his soul still his own, he can still be forgiven and be at the Emperor's side again and together they can beat back Chaos. Magnus' anger is fizzling out, like a son who knows he’s done bad and just wants to be with his father again, and starts to seriously consider Emps’ words. Big E tells Magnus he'll be in charge of a new legion of warriors, implied to be the Grey Knights. Magnus asks what the cost of salvation is. Big E says that he'd have to give up the Thousand Sons, as they are too corrupted to save and must be purged. Magnus' fatherly instincts are too strong, he won't sacrifice his sons, and this pushes his rage button HARD. He’s furious that his father make such an insulting and impossible offer, and even more furious that he was actually tempted for a second to take it. He throws his charged up spear at Big E while he’s defenseless. The spear is intercepted by Vulkan's giant hammer before it can land.
Magnus and Vulkan have their battle. Magnus is winning, but a bunch of Space Wolves and Salamanders distract Magnus just long enough for Vulkan to land some serious blows. Despite the horrific injuries he sustains, Magnus just regenerates them and grows even more wrathful. Enraged that he almost let himself be swayed by the words of his brother and father, wanting revenge, and doing whatever it takes to save his sons, Magnus fully commits himself to Tzeentch and transforms. Now a daemon prince, his power soars to even greater heights, but he's kicked out of the Palace from the anti-Chaos shield. Outside again, he pledges to support Horus to the end.
Malcador gets resurrected because his fellow Perpetual friend sacrifices her own life-force to restore him when his own could not, at the cost of her own. After all, Mal needs to be alive to temporarily take Big E’s spot on the Golden Throne so he can fight Horus in the final Siege book before he dies for good.