I seem to remember that there was originally a full fledged mission in between the SR1 biting the dust and Shepard reawakening, in case anyone has wondered where the extra voice acting comes from. I'm not spoilering anything here since none of it made it into the game and it doesn't actually delve into any late game plot.
You started off as Legion, unfolding from a cargo box that you had sneaked into aboard the Shadowthrone, the Shadow Broker courier frigate with your body on board. After a few minutes of sneaking, you start hearing gunshots and reports of an intruder over the intercom. Eventually you met Liara, who was on her own mission to steal the corpse. After a heated mexican stand, Liara and Legion teamed up to steal the corpse on agreement that she got to take it where she wanted(Cerberus). Over the course of the mission, you played as Legion and inquired about Shepard's decisions based on your investigations. In this manner, it was originally set up to allow you to customize an ME1 game's choices through your dialogs with Liara.
After a few short gunfights, they were to finally get to Liara's small infiltration ship, but not before having to take of Shepard's armor off order to get him/her into Liara's containment field to keep the body from falling apart. On his way into the ship, Legion was to be shot and disabled as well as given his iconic wound. It was then to shift into first person and you see Liara close the door and launch her small ship from the airlock. A -NO FEED- was to come up on the screen in red and then fade from view, followed by Shepard fading in and out and seeing Miranda. The game then continued as normal until you got to the first missions.
On your way to Omega for the first recruitment, you picked up a distress signal from the Shadowthrone. Miranda was to recognize it as the ship that your corpse had been stolen off of. It's beacon suggested that it had been adrift for nearly two years. Knowing that agent that had bought you from had left the ship functional and suspecting that it had something to do with the disappearances, she suggests boarding the ship to investigate. Once on board, you discover that Legion had reactivated and repaired himself with the armor that had been pulled off of you. He had then hunted down and killed the entire crew but had accidentally caused irreparable damage to its drives. To save energy in the powerless ship, he went into a hibernation mode. You find the hibernating Legion in the engine room and remove him, leaving you with the choice of whether or not to activate him.
In the end it was scrapped because it was seen as too confusing for players new to the series. It was also redundant to have Legion tell his unique story to Liara in the beginning and then to Shepard again less than two gameplay hours later. Additionally, it was seen as too different from ME1 to have the player's first shooting battles be as a Geth against humans. The comics were given an OK instead to fill the gap and some friend for Liara was created to take the place of Legion.
A lot of assets, like Legion's Shepard Armor repair or much of the unused dialog, were left in game with little or no explanation. In the case of the former, it went from causing a long conversation about how he stalked the crew of the Shadowthrone to "No Data Found." Much of the lost dialog, like his lines before he can be acquired, were just left since he would never be there to trigger them. Other dialogs, for instance he had a long dialog with Liara if you brought him to Illium, never even made it off the paper. Most of the assets were retooled though, like the SR2 Cargo bay that was originally Legion's starting point in the mission. The Crashing Ship mission is almost a direct usage of most of the Shadowthrone's assets, complete with the engine room where you were supposed to find him in up where you now turn the engines on.
Additionally, Veetor was a relatively late addition to the game. Originally you met Tali on Freedom's progress and she joined you from there, but that was scrapped for reasons I don't know. Similarly though, many of her lost dialogs were just left in since she would never be there to trigger them without hacking the game.
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