The Return of Haruhi Suzumiya Theatre (帰ってきた涼宮ハルヒ劇場) is a short story that was published in the June, 2006 edition of The Sneaker. It is the sequel to Haruhi Suzumiya Theatre. No other parts of the story have appeared or been translated.
The SOS Brigade were stuck in a simulation, apparently of an RPG or video game. Having failed in their last mission to rescue the prince and princess from a demon lord, now they had to do the same thing, only rescue the emperor's children from space pirates.
The Haruhi team of the Galactic Regional Observation Conclave's Patrol Force, a sci-fi team, had only a small spaceship dubbed "The Schismatrix". Nonetheless Haruhi Suzumiya was confident the space pirates would be easily defeated, and of course she'd take all their treasure.
Kyon inventoried the team roles. He was the pilot, Haruhi was the commander, Yuki Nagato was the radar operator, Mikuru Asahina was the communications officer, and Itsuki Koizumi's role was apparently navigator. Nagato searched for pirates, while Haruhi sent Asahina to get tea.
Koizumi researched the history of the empire. He could find no information on the "Sargasso Sea". There used to be one empire, but it had since split into the United Galactic Conquest Empire, the Orthodox Galactic Empire Exiled Administration, the Galactic Empire Federation, the Holy Galactic Empire, the True Galactic Empire, the True Galactic Empire Border Regions, the Galactic Empire Independent United Constitution, and others. Koizumi said the "pirates" could actually be the regular military forces of another nation.
Haruhi randomly picked a point on Koizumi's star chart and said to fly there. Kyon, who thought he lacked the knowledge, still had the ship jump into hyperspace.
An hour later, they were captured by tractor beams projected from a massive fleet, which was confused by their appearance. A communications was made—a man looking like the forest sage (from Haruhi Suzumiya Theatre), but with a military uniform, told the heroes they shouldn't have jumped into the fleet without warning, as that risked a nuclear explosion. The sage said they (the heroes being of the Galactic Regional Observation Conclave) had no business there. He identified himself as the commander of the Neo Orthodox Galactic Empire's Third Fleet, and they were conducting military exercises, so they needed to leave.
Koizumi identified their position as near the border between the Neo Orthodox Galactic Empire and their own, but in the Neo Orthodox space, away from the kinds of shipping lanes where military exercises were permitted. No such exercises had been scheduled either. Instead, they were trying to sneak into the Fifth Empire.
Haruhi threatened to reveal their invasion fleet unless he told them where to find the pirates. The "sage" said Captain Beyond's Upperground Pirates had probably done the kidnapping. Haruhi said the "sage" was probably the one who had done it instead, disguising one of their vessels as a pirate vessel.
The "sage" was upset they had figured out (really guessed) his plan, and would silence them. The tractor beam began pulling them into their hangar. Koizumi told Nagato to find the prince and princess, while the Schismatrix "infiltrated" the enemy flagship. Haruhi wanted to take over the flagship's bridge, tie up the sage, and force him to hand over the children. Unfortunately the Schismatrix was surrounded by guards.
Koizumi asked Nagato to search the crew list for the prince and princess, which she hacked from the enemy. It showed most of the crew were military. Accommodations had been made for two "new" crew members in a large room, on the very flagship the heroes were now surrounded in (Nagato was able to pull up the flagship's schematics as well). The room was closer to them than the bridge. Nagato asked what they should do.
Koizumi said this fleet needed to move "silently", so he told Nagato to force them to reveal themselves. She activated their ECMs. A Fifth Empire fleet hastily arrived and began attacking the Neo Orthodox ships. The guards moved away as their ship fell into confusion.
The space patrol left the ship. Haruhi ordered them to set their weapons to "P" (for paralyze). Nagato led them unerringly to the prince and princess. Haruhi set her weapon to "infrared" and melted the door. The royal prisoners were shocked and confused.
The space patrol took them back to their ship. Every once in a while, they would be attacked by "grunts" but they were all defeated by Nagato's pinpoint shooting. Back on their ship, the space patrol blasted their way out of the enemy flagship with some kind of particle weapon.
Haruhi ordered Asahina to contact the emperor. The emperor was delighted, and said they could name their reward, but he was currently commanding a space battle and they should take the children to a safe place for the time being.
Unfortunately, the two children turned out to be robots, as Nagato quickly discovered. The two robots collapsed. Koizumi believed this was the reason they were so conveniently found on the flagship. The two fleets continued to blow up each others' ships, and soon Nagato announced that the mission had been accomplished, and a penalty had been assigned.
The heroes appeared in a western setting. The story ended there...