Weir went Passive-Aggressive on him to show her displeasure against his “Outright murder” of the Genii, and approval of everyone else on the city for his actions. And was not happy that he snubbed her actions as being “unproductive” to the laughter of everyone who witnessed it.

Four weeks later an apologetic Colonel Ellis personally handed over a large box to John in front of Weir. A large envelope to Weir he had her sign as having acknowledged receipt of, and acknowledgement of the orders from the President and the Head Representative of the IOA (Her ultimate bosses), and that she would OBEY those orders.
She tried to refuse till Ellis had his marine security force surround her, and only then did she sign his clipboard. He looked at and lined through. Stating she signs her full and actual name or be arrested.

She looked at those watching in the gate room and huffed before signing again and handed the clipboard back for him to look at. Then he got an inkpad and had her ink both her forefingers right after her signature for verification purposes. Saluted her and beamed back aboard to her huffing annoyance as she stomped back to her office and slammed the door.
Then her lamp hit the door and shattered at the same time she bellowed a scream of outrage. And silence.

Seems she received orders she didn’t like.
It also seemed as though she did not appreciate the introduction of a new psychologist who she had no control over as he was military instead of civilian. And dealt specifically with combat trauma. And Heightmeyer’s and Weir’s orders now stated he was the mental health doctor for all military and security personnel, and security needs. NOT the civilian contractor.
And since he was in the military, he did NOT fall under the purview of Weir like Heightmeyer did, but Sheppard and so she had no control over him. Plus, he had combat experience and a backbone to back up what he said. AND had the official capacity to pull anyone, even the leaders, if he felt they were compromised.

His first patient was John. But every single member of the military was lining up to get at least one appointment with him instead of the old doc.

To the surprise of Landry, Landry was forced to allow R&R rotation of every member of Atlantis for a time period listed by the new doc for combat mental health reasons until cleared by SGC’s physicians to return to the city.
Including the Heads, with Sheppard starting. And ordered home to his family’s care. Then Weir when he returned, then McKay.

%%%%

It took a month to stand down from battle readiness for John while he was at his family home. Because of need, his father and brother had been read into the program, with Dave now on hand as the program’s JAG representative. And this allowed access for John to get his therapy at home with the doctors beaming in for each appointment each morning. Then downtime to get over the sessions, then time with his family.

It did not last though as the city was slowly shutting down without him there, and so, he was soon gating back to Atlantis with his updated records after a week’s worth of apology meetings with O’Neill the SecDef, and the President. And a shiny new Medal of Honor ribbon to go on his dress uniform while his actual medal held pride of place above his father’s fireplace. And right next to it was the original signed letter from the sitting SecDef and President as CoC stating then Major Sheppard was in the right for his actions in rescuing the bodies of his teammates and making sure the enemy did not gain access to American made weapons or technology. And the black mark on his record was officially expunged.
He hadn’t been pardoned for the incident; he was found to be not guilty after an official inquiry finally happened into the event.

John had a copy for his SGC files and O’Neill made sure to personally hand a copy over to Landry and had him sign a prepared statement that he understood what it meant. And O’Neill popped over with a copy for Weir doing the same so neither one had that mark to hold over him anymore.
They also had to sign another statement showing they had read and understood the significance of the MoH given to him over the Genii Invasion. And what that statement by those in the know said about his involvement in it.

Weir was not happy.
Nor was she happy about the mail stating that he and Rodney were “Mission Critical” but left her out of that statement. Showing where she stood in the pecking order.
Letting everyone know she wasn’t happy as she had been ordered back to Earth for her own downtime and exams.

She never returned again. And was replaced by Colonel Carter of SG-1, in time for Rodney’s downtime right after Doranda.
Thankfully it hadn’t gone as bad this time around as last time without the pressure from Weir and John stopping it before it got out of hand and destroyed everything. But still, Rodney needed the downtime badly and was allowed as much as he needed.

And, with no Weir egging Carson on, there was no Wraith Michael either to John’s relief. In fact, Carter and the returned Rodney went to town on the experiment files – and non-files – of every person – including medical – in Rodney’s department now that Weir wasn’t stopping him.
Carson was arrested for his illegal experiments and sent home via the gate with Biro taking over his position.

Therapy continued without the outside passive-aggressive negativity from his nominal superiors, and he relaxed more into his situation as 2iC to Carter’s Command. And Lorne being his second now that they had an actual chain of command. New, practical scientists were cycled through to replace the pure theorists, and more infrastructure staff were added as well. Actual security personnel, instead of rotating military through, logistics, supply and everything else and everyone else that they had badly needed was starting to come in now that Weir and her network at the IOA was gone.

During the time he had been down or off the city on Earth, Teyla had moved to Lorne’s team to continue doing her job as Head of her people and in charge of trade. Something that was now split depending on assignments as his team now did a lot of Search and Rescue work because of his past Recon missions. Or Intelligence gathering missions. Usually, Ronon was the only regular he had on his team with others coming and going depending on what was needed. With Carter he was collating everything later with the two resident aliens to put things into perspective and figure out where they needed to be next. Making for smoother non-combat missions, or special combat mission to take out problem areas now that they were on a war footing. Receiving fewer friendly bodies to send home in bags now than when civilian Weir ran things.

City stress levels were way down because of it and the new security measures of a beta and gamma site being put up and all missions going through the beta site instead of the city.

Atlantis was content now, and he was content.

Life was good.