'A Thousand Sons' tells of Magnus' psionic trip to the Emperor's palace, and in that it is revealed that Magnus never had the chance to actually deliver his message. Also, it tells of how he utterly destroyed the Emperor's project.
If the project is wrecked, either the Emperor was sitting sulking in his dungeon, ignorant of Horus' imminent betrayal, or he was fighting off interlopers from the warp who were capitalising on the rent in real space that Magnus had torn open, and so couldn't get out himself. Was this not, after all, where Sanguinious was later to fell a horde of chaos minions whilst the Palace above was besieged? Though that then leaves open the matter of what the Emperor was doing from when Sanguinius took over the guard?
If the project is wrecked, either the Emperor was sitting sulking in his dungeon, ignorant of Horus' imminent betrayal, or he was fighting off interlopers from the warp who were capitalising on the rent in real space that Magnus had torn open, and so couldn't get out himself. Was this not, after all, where Sanguinious was later to fell a horde of chaos minions whilst the Palace above was besieged? Though that then leaves open the matter of what the Emperor was doing from when Sanguinius took over the guard?