The B Team Storyline
LOTM: The New Multi-Universal War
Luna returns here to help the heroes against the empire. She lead a small resistance in Ponyville.
Fire Rebellion Storyline
Order of the Just
"It takes a lot of heart and honor to serve her in the Order. However, if you want your membership here to go smoothly, you need to keep the chaos in your subconscious at bay if you want to avoid any trouble with the ones who swayed her once before. Don't expect Luna to be soft and sweet all the time. Her duties as both the Princess of the Night and Head-figure of the Order require her to be assertive and intimidating when the shit hits the fan. You keep performing right, you might just become her protege. - Elias T. Walker's outlook on Princess Luna.
After being freed from the Nightmare Forces' grip and proving herself to the residents of Ponyville, Princess Luna was gifted the position of leader of the Order of the Just by Pelinal Whitestrake, the crusader that once defeated Umaril the Unfeathered and the Order's founder.
She, along with her sister, Princess Celestia, and Revan were able to restore the Order's former stature. Eventually, major hero teams such as the Brotherhood of Steel and Fourth Echelon started contributing members to the cause.
After becoming full leader of the Multi-Universal United Government, she had given full leadership of the Order to Revan, which the latter had then given to Fire Lord Izumi.
Mervamon and Ponydramon
Princess Luna is a member of Team Ironhide. Like her sister, she too has a powered up form.
Luna and Twilight share a good friendship. Twilight was responsible for Equestria's new found love and understanding for Luna after being purified.
Revan and Luna share a friendly relationship as the former is the second-in-command of the latter.
Elias is Luna's top enforcer. Luna is impressed with Elias' performance and leadership skills.
Luna has a liking for Iroh's wise and calm outlook and his positive connection to the Spirit World.
Luna is impressed with Takuya's sense of Justice, but sees his overconfidence as a drawback.
Sam is honored by Luna for his team's role in taking down Majid Sadiq.
Luna sees Mikey as a great candidate for membership in the Order.
Luna hopes that Shoutmon will achieve his goal to become the King of the Digital World to protect its inhabitants, but knows that he still has much to learn.
Due to Caboose's mental inabilities, Luna tends to watch over him to make he doesn't accidentally hurt anyone or himself or damage anything crucial.
Luna has a so-so relationship with Epsilon-Church due to his actions to kill the Director went against several laws. Luna almost had to intervene with a problem soon after the Director's death.
In the Fire Rebellion storyline Agent Michigan is the captain of Luna's royal guard.