The Massacre at Eridanus Secondus was a minor event in the Human-Covenant War that resulted in the destruction of the Eridanus Rebels. It is most notable for the involvement of the Gettysburg-Ascendant Justice and Dr. Halsey's kidnapping of Kelly-087.
Background
Spartans and Colonel Watts
In 2525, the Spartan-II unit's first assignment was to infiltrate the Eridanus Rebel's base and capture Colonel Watts. The extraction component of the mission did not go smoothly and they were forced to kill several rebels and destroy the base's hangar. Of the 5 members of the team that were involved in that mission, 4 participated in this battle including John-117 who suggested the location.
Raid of Reach and Earth
During the Raid of Reach, Cortana intercepted transmissions between Covenant forces that indicated that the Covenant were planning on attacking Earth. They intended to rendezvous at the Unyielding Hierophant before finally attacking the Terran homeworld.
However, the Raid of Reach and the subsequent battle in the slipspace anomaly took them well beyond UNSC controlled space and severely damaged the Gettysburg-Ascendant Justice. Looking for a place to acquire repairs, John-117 recalled his earlier mission to the Rebel base and suggested it.
The Crystal
The Forerunner Crystal that was found on Reach and caused the slipspace anomaly posed a problem. While most slipspace movement could go undetected, the crystal sent out large doses of radiation that could be detected by the Covenant, effectively allowing them to track its movements. As such, the arrival of the Gettysburg-Ascendant Justice in the Eridanus system spelt the death of the Eridanus Rebel base.
The Battle
Scouting Patrol
After negotiating a meeting, Vice Admiral Whitcomb warned Governor Jacob Jiles that the Crystal meant that the Covenant would soon be arriving. Governor Jiles had just asked for proof of this claim when a Covenant Cruiser emerged from slipspace. After quickly assessing that both sides didn't have nearly the armed capabilities that they initially thought, Admiral Whitcomb tried the only solution available to him - the firing of a Plasma cannon. However, the Plasma Cannons magnetic coil failed, making the plasma blast shoot straight into the Gettysburg's hull rather than at the Covenant warship.
It was suggested by Spartan-117 to try using the Magnetic coil on the Gettysburg to direct plasma from the Ascendant Justice. This worked and successfully destroyed the Covenant Cruiser, but at the cost of destroying the turret that had fired the shot.
However, the scouting report proved that a Covenant fleet was coming and Governor Jiles agreed to help the UNSC forces. With the help of the rebels, they began repairs on the two warships.
The Commandeering
Dr. Halsey, who had spent large portions of her career wrestling with her guilt, had decided to pursue her own agenda to try and save the Spartans. To this end, she sedated Kelly-087 and gave the Forerunner Crystal to Corporal Locklear with explicit instructions to destroy it.
With the Corporal's help, she was able to move the Spartan onto a Chiroptera class vessel which she then used to flee the system. This move frustrated both Governor Jiles, who felt it was a betrayal of trust, and Admiral Whitcomb.
The Main Force
However, neither were given much time to complain about the matter, as a large Covenant fleet arrived in system shortly after the Doctor's departure. Initially, 2 warships entered the system, prompting the coupled Gettysburg-Ascendant Justice to leave the Rebel base, though without the evacuees on board.
By the time they were clear, a total of 30 Covenant warships had entered the system from 3 separate vectors. Whitcomb, feeling his duty was to Earth, not the rebels, ordered an immediate retreat to slipspace, leaving the helpless rebels to their doom.
Aftermath
Rebels
It is assumed that the rebels were destroyed by the Covenant forces after the retreat of the Gettysburg-Ascendant Justice. No mention is ever made of any refugees on board the Gettysburg-Ascendant Justice.
Operation: FIRST STRIKE
The Gettysburg-Ascendant Justice would take a detour to the Covenant rendezvous by Unyielding Hierophant in Operation: FIRST STRIKE, eventually annihilating the vast majority of the fleet.
Dr. Halsey and Kelly-087
The Doctor and Spartan would eventually wind up over the planet Onyx during the Battle of Onyx, a battle they would play a major role in. They would eventually be joined by several other survivors from this battle.