So because one of my line managers at work is absolutely off the walls fucking nuts, I am altering my lore last second to make the whole "Commander Tower retires, and a new guy takes over GUN" thing happen sooner. It happened previous to the events of WtDMtN, and has been an ongoing issue for a while now.
So Tower is succeeded by a guy named Commander Wilson, and Wilson is fucking crazy. He has it in his head, for some extremely bizarre reason, that because he's the Commander of GUN, he also gets to order around the Restoration. So he's constantly sending Jewel memos and shit.
But he's not just ordering her to do shit. He's scolding her for not following the orders he sent her previously, but he never sent her those alleged "previous orders". Jewel and Lanolin are CONSTANTLY telling him they have no idea what he's talking about, and also that GUN and the Restoration are two separate entities. They do not answer to him, they have no intention of answering to him ever, stop sending half a thousand messages to them a day.
Rouge (who's kinda playing double agent in all of this, she tells the Restoration what top secret stuff GUN is up to) is also completely in the dark. She has no clue what the fuck Wilson is on about, she never knew what the fuck Wilson is on about, just keep telling him to lay off the drugs and get lost. Maybe he will eventually.