With such a mind in the warp, it was not long until the Emperor noticed him. When his fleet arrived, it as was if the two had known each other for years, although not in the flesh just in the mind

The Thousand Sons Magnus inherited were rife with psychic mutations, being based on Magnus' genes. He took them in as his own and began training them in the ways of the psyker. Individuals from within the Imperium who were fearful of these rampant mutations began to voice their opinions openly, but Magnus silenced them. The further from Terra the crusade went, the more strange warp powered creatures they came across. This naturally made Magnus look bad, his control of the warp being similar to these creatures. Leman Russ and Mortarion both distrusted Magnus due to his use of the warp and because of his use of deceit where they would have used overwhelming numbers.

To solve this dispute, the Emperor called for a debate on the use of psychic powers. They gathered on Nikaea and the Emperor presided over the debate. The results meant that sorcery was illegal, but psykers were to be trained for the benefit of the Imperium. Magnus was not happy, but was forced to comply, which he did. It would be the last time Magnus and the Emperor would meet however.