On each one of your planets, after colonizing it, you can have a commander (attached to the planet)
You can choose beteen nine different commanders, each one of them giving you a specific bonus.
The commanders have 4 levels.
You MP (Mother Planet) commander will always be level 4.
When choosing him, you will know his level :
How to change your commander
You can, via the consortium, changer your commander for 8000 dark matter. Beware, he does not keep the level he previously had.