Executor Artanis and Judicator Aldaris had traveled to Char to arrest the rogue High Templar Tassadar for treason, after he disobeyed orders and allied with the heretics, the dark templar. Artanis sided with Tassadar in this and went to the surface of Char to find Dark Prelate Zeratul, leaving Aldaris to return to Aiur and inform the Conclave of Artanis betrayal.
Artanis, Tassadar and Zeratul returned to Aiur, and were contacted by Fenix, a comrade of Artanis and Tassadar believed dead in a zerg attack. Fenix announced he had been preserved in a dragoon exoskeleton , and warned them that Aldaris and the Conclave intended to arrest them when they landed on the planet, and execute Zeratul. Though surprised at the Conclave's blind zealousness, Tassadar resolved to go to war with the Conclave if it meant protecting the dark templar, and Fenix prepared to aid him against their forces.
Tassadar, Zeratul, and their followers landed on Aiur and were met with a hostile welcome from Aldaris, who demanded their surrender. Tassadar refused and the Conclave attacked. The warriors fled to a base secured by Fenix, and prepared to strike back against the Conclave. The resulting battle destroyed Kor-shakal, killing all Conclave members within. Though their forces proved victorious, Tassadar was disgusted by the sight of protoss warriors fighting each other on their homeworld, and surrendered to the Conclave.  Aldaris took him into custody to stand trial. Fenix and Artanis were able to escape safely, and in the chaos Zeratul and the dark templar vanished.
The player begins with Tassadar, Zeratul, and four dark templar in a field south of their base, and should immediately retreat them. The player's base is very well established, with an easily defended choke point on high ground garrisoned by photon cannons, the rest of the base is walled off, and the player got a wealth of resources with 2,500 starting minerals and gas. The player should begin by warping in several more gateways and stargates, and can also warp in all other available structures so they can focus on building up their army. Several forges to research numerous upgrades at once may also be wished, and the player will later need a robotics facility and observatory.
The hero units the player has are very powerful and should be used liberally to defend. The Conclave attacks with zealots, dragoons, high templar, carriers, reavers, and scouts, and the latter will attack over the walls, particularly at the far eastern end of the player's base. The Conclave will send observers with each attack, revealing the dark templar, so the player should be careful with them; the normal dark templar can die without penalty, but Zeratul cannot. There is another mineral field east of the player's base, and they should claim it once their standing army is large enough to defend it.
With their economy established and base built, the player can turn their attention to the mission objective. The mission is won when either the Ara Tribe or Auriga Tribe command no nexuses. The lone Auriga base far to the south-east is very large and very well defended with photon cannons, reavers, dragoons on high ground, and narrow passages. Attacking this base is ill-advised, but if the player do so they should use a large fleet of scouts. The two Ara bases are considerably easier targets, and the player should focus on destroying them.
A large ground force of zealots, dragoons, and reavers should be built, and all their upgrades researched. The Conclave commands arbiters, so the player must include observers in their army to nullify their cloaking. The western Ara base is lightly defended behind a wall, while the eastern base has a bridge heavily guarded by photon cannons, but another bridge south of it is entirely undefended. The player can strike either base first. With two expansions and several unit-producing structures, the player can build up a massive army to sweep their enemies. When the two Ara nexuses are destroyed, or the lone Auriga nexus is destroyed, the mission is won.
A quicker and easier way to win the mission can be done using Zeratul and the dark templar. Directly south of the player's spawn position, the player can move them across a bridge and to the southern edge of the map. Here there is a very narrow back entrance to the Auriga base. An observer patrols here, but the player can move their dark templar past it and it will not pursue them. Directly east of this entrance is the Auriga nexus, and the dark templar can swiftly destroy it. An observer and defending units will investigate, but they will not arrive in enough time to stop the dark templar from destroying their target.
- Blizzard Entertainment. StarCraft. Vivendi Games. Mission: Choosing Sides (in English). 1998.
- Tassadar: "Fenix? It can't be! The Executor told me of how you fell before the Zerg. How is it that you live and breathe?"
Fenix: "Ha hah... Well, after my unfortunate defeat, my ruined body was recovered by our brethren. I now reside within the cold, robotic shell of a Dragoon."
Tassadar: "Old friend-would that this never came to pass..."
Fenix: "Nonsense! There is no shame in defeat so long as the spirit is unconquered, and I am still able to serve Aiur to a degree."
StarCraft. Vivendi Games. Mission: Homeland (in English). 1998.
- Blizzard Entertainment. StarCraft. Vivendi Games. Mission: Homeland (in English). 1998.
- Golden, Christie (June 30, 2009). StarCraft: The Dark Templar Saga #3: Twilight. Simon & Schuster (Pocket Star). ISBN 978-0-7434-7129-9.
- Tassadar: "Executor! Aldaris! This madness must stop! The sight of my brethren slaughtering one another is more than I can stand. Though I fear you would doom us all, Aldaris, I surrender myself to the Conclave. En Taro Adun, Executor. Don't give up the fight!"
Aldaris: "Tassadar of the Templar, by your actions you have severed yourself from the mercy of your brethren. You refused to destroy the Terran worlds as was commanded. You have questioned time and time again, the sacred will of the Conclave. And you have abandoned your Homeworld in its darkest hour. Most grievous of all is that you have allied yourself with the blasphemous Dark Ones, and learned to utilize their profane powers in tandem with our own! What say you, oh fallen Templar?"
Tassadar: "Aldaris, I submit myself to the Conclave's judgment. But know this, given the same choices again, I would surely have made them. I have sacrificed all that our world might live. I have sullied my honor, I have discarded my rank and standing, and I have even broken our own most ancient traditions. But never think that I would, for one moment, regret my actions. For I am Templar, and above all else, I have sworn to Protect our Homeworld 'till the end."
StarCraft. Vivendi Games. Mission: Homeland (in English). 1998.