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AUTHOR'S NOTE: Since we're going to touch on the same subject here, let me answer some of the responses for the last chapter:
Jenna called it perfectly. It doesn't matter if we're talking about two different services with two different missions. It doesn't matter if they come from two different countries or two completely different civilizations. It doesn't matter if one isn't a military organization. It doesn't matter what Starfleet Command "wanted", or what "Enterprise's" writers "intended". As long as both Starfleet and the Military Assault Command use Western Military Style Rank Structures (and they do, and Starfleet ALWAYS has), then ranks in one organization will have equivalent ranks in the other. Hayes is equivalent to a Starfleet Lt. Commander. Lt. Commander beats Lieutenant. Hayes outranks Reed. Period. End of Debate. And since Hayes outranks Reed, no matter what convoluted BS the Writers, Starfleet, Archer or anyone else comes up with for explaining why Hayes should follow Reed's orders, there is No Law On Earth (or any other planet for that matter) that would require Hayes to call Reed "Sir". He has, and this not just an honest mistake on the writers' part. This is evidence of a blatant disregard for reality and an insult to the viewers' intelligence.
Why do I say that? In the "Deep Space Nine" Dominion War Story Arc, when several Cardassians wanted to revolt against Dominion control of their empire they asked the Federation for advisors to help plan and run an insurgency. The Federation turned to the Bajoran Militia, and the chief advisor the Militia offered was Kira Nerys. Since the Federation was worried that Cardassians wouldn't accept help from a Militia soldier, they gave Kira a Starfleet Commission as a full Commander. Commander is equivalent to the rank she was promoted to when Sisko left, which was Lt. Colonel. Two different organizations, two different missions, two different civilizations, yet since both Starfleet and the Militia used rank structures any American, Brit, Canadian, Australian, New Zealander, etc. would easily recognize, Starfleet was able to take Kira into the chain of command while maintaining her rank, authority and privileges.
That means that there is at least One Star Trek Creator around that understands everything I've been saying. It is the height of illogic to assume he managed to keep all this secret from the rest of Star Trek's staff, or that none of the others are capable of figuring it out for themselves. Hayes deserves all the respect he would get from Reed if Reed were a MACO at his current rank. He hasn't gotten it, and a truly realistic depiction of the outcome of their clash would have Reed facing demotion, or time in the brig, or BOTH for some of the crap he's pulled.
With all that in mind, I offer the following alternate scene...
"REALITY CHECK", by DARRIN A. COLBOURNE
"Chain of Command"
She would never admit it, of course, but T'Pol was experiencing what was, to her, an extreme bout of discomfort. When she first joined the ENTERPRISE's crew she had expected to be subject to an inordinate amount of interest on the part of the Humans she'd be working with. She'd never sought the attention, naturally, and was inwardly glad for two things: Humans adapted quickly enough in some circumstances that she would eventually cease to be a novelty, and until then the Humans' curiosity would be divided between her and Phlox.
No such comforts were available to her in this instance. She was the center of everyone's attention now - including Phlox - by Captain Jonathan Archer's design. The event about to take place demanded it. The Crew's Mess was cleared so that all non-essential personnel could attend the ceremony. Archer and T'Pol were standing at the center of the room, surrounded by the rest of the crew. The Captain was giving a speech, but T'Pol was lost in her thoughts and was tuning him out.
She'd protested what was about to happen, but Archer had been adamant about doing it. She'd tried to use logic to make her case, but - surprisingly - his argument had been just as logical. In fact it was more logical, since she'd eventually given in to it.
Suddenly she felt an itch, and it took all of her self-control not to scratch it. She wondered idly how long it would take for her to adjust to wearing a Starfleet Uniform. The blue jumpsuit was certainly looser than her usual garments, but that didn't necessarily make it more comfortable.
"SubCommander T'Pol." Archer said. T'Pol came to full attention in front of him, putting her thoughts aside. As of this moment, none of them mattered. She looked him square in the eye as he continued.
"For faithful and diligent service to this ship and her crew, by the authority vested in me as Captain of the Earth Starship ENTERPRISE, I hereby award you a commission in Starfleet and a promotion to the rank of Commander, with all rights and privileges attaining."
With that, Archer came closer and proceeded to attach three rank bars to the collar of her uniform. The bars were provided by Trip Tucker. When he found out what Archer was planning he'd immediately offered his spares as a gift.
When he was done, Archer stepped back and offered his hand. "Congratulations, Commander." He said with a smile.
T'Pol took the hand and shook it. That's when the gathering erupted in applause. When they broke T'Pol turned to face the audience. She bowed her head lightly in response to the smiles and cheers all around her. For the moment she was at a loss as to what else to do. She couldn't recall ever being the recipient of such adulation, and even then Vulcan accolades were hardly so...boisterous.
"Thank you." She said to everyone in a strong, clear voice. This caused the applause to die down. "I'm grateful for your appreciation and respect, and am honored to be counted as a member of such a fine crew. Company - As You Were."
The First Officer had spoken. The gathering broke up with some parting well wishes for T'Pol as the crew returned to their respective posts. A few lagged behind to offer more personal congratulations. One was Ensign Hoshi Sato.
"So, how does it feel to officially be the First Vulcan in Starfleet?" Sato said, then regretted her choice of words. "Sorry. I guess 'How does it feel' is kind of a silly question, huh?"
"On the contrary." T'Pol said. The idea that she didn't feel at all - rather than suppressed what feelings she had - was a common misconception among Humans. "As I said, I feel honored and grateful. I am also somewhat apprehensive."
"Why?"
"When he first made his intention to give me a commission plain, I reminded him of his reluctance to have me on his ship when we first met, and that several members of the crew shared that reluctance at the time. Now it is not just a matter of a single ship. Starfleet has never had a non-Human member in its history. Being the first is an honor, but it is only a welcome honor if the Humans that I work with are willing to accept me as a peer."
"But we already accept you here. For this crew there is no real adjustment to make. You're one of us, plain and simple. All the uniform does is seal the deal."
T'Pol gave Sato a curious look. "That is almost exactly what Captain Archer said."
Sato gave T'Pol a wide grin. "I always knew he was smart."
As Sato and T'Pol talked, Archer accompanied Tucker to the Engine Room. "You're sure you're okay with this, Trip?"
"It's like I said before, Cap'n," Tucker said, "being First Officer is a full time job, and I already have one of those. T'Pol's been doin' hers for the past couple of years now. It's about time she had a rank commensurate with her duties." Besides, he wouldn't say, now that he and T'Pol were the same rank their massage therapy sessions wouldn't feel quite so much like "unlawful fraternization" to him anymore.
"I should've done it sooner." Archer said. "Maybe she would have felt more comfortable dealing with the situation between Malcolm and Hayes before it got to me."
"Well, it's done now. An' I don't think either of you will have any trouble with Malcolm from now on."
"Have I got your word on that?"
"I don't know what you said to him, but he seemed to be a might upset when I spoke to him last. Still, he also sounded like he was willing to be a team player for the rest of the mission." When they reached Engineering, Tucker said: "Was there somethin' you wanted me to do, Cap'n?"
"I need your input." Archer said. "We may be facing more serious attacks soon, and there are a few things about the ship that have been bothering me..."
FINAL AUTHOR'S NOTE: The second he found out that T'Pol was giving up her Vulcan commission to serve in ENTERPRISE on the mission to the Expanse he should have taken her aside, handed her a jumpsuit and rank pins and said "Welcome to the Club." There should have been no debate of any kind.
ENTERPRISE is a ship at war. Keeping T'Pol as First Officer in her current status is tantamount to making a Civilian from a Neutral Country Executive Officer of a U.S. Aircraft Carrier on its way to the Persian Gulf. Nothing like that has ever happened in reality and it never will.
The First Officer/First Mate/Executive Officer of any ship has a primary function: It is his/her job to maintain loyalty and discipline among the crew. How can Archer to trust T'Pol to do that job when, with no official ties to him or the crew, he can't even guarantee he'll receive loyalty and discipline from her? (Remember, in "Damage" T'Pol admitted to shooting up a substance that A) Makes Vulcans Crazy and B) the ship needs to survive the Expanse.)
And before anyone says it, Yes, it would mean that we would no longer see Jolene Blaylock in the Pretty Pastel Catsuits, but we already know from "Twilight" that she still looks hot in a Starfleet jumpsuit, so let's get her in one already.