On Shadow the Hedgehog, in the ARK during a flashback, it is shown that GUN soldiers are invading and destroying the space colony. Also, the Commander of GUN reveals himself as being Maria's brother. If this is so, then why is he the Commander of GUN, if he knows that they were the ones who had infiltrated the ARK?
The Commander never reveals himself as Maria's brother; he just considered her like family. Also, he thought that GUN had ultimately done the right thing back then, as he believed Shadow was the cause of all the trouble and thus ultimately responsible for anyone who ended up dying during GUN's invasion.

~ Crazy C Lea