I dont really understand how mission DLC is gonna work for this game. After u complete it the game just ends and the different hubs are only available at certain times depending where u are in the story..

Probably explains it in the opening of the DLC. Maybe you'll choose the DLC in the menu and jump right in.

looked like they take away all your augmentations so it could be an independant character with back to the start augs.

It's Jensen, and yeah, his augs are disabled or removed.

In The Missing Link. During Adam's quest for the truth in Deus Ex: Human Revolution, he mysteriously vanishes for three days. Where was he? What did he find out? The Missing Link reveals it all.

After being tortured by Belltower agents and having his augmentations disabled, Adam Jensen must rely solely on his basic capabilities to escape from a freighter, destined for an unknown location. While fighting for his survival on the ship, he uncovers another layer to the conspiracy that he never would have suspected. As Adam, befriend new, mysterious allies and fight ruthless enemies to discover what was happening in the shadows during the events of Deus Ex: Human Revolution!

-New layers of conspiracy unveiled

-Sprawling new environments

-Brand-new characters to interact with

-Rebuild Adam's augmentation set from scratch. Build up a brand new Adam!

It looks interesting, but the game didn't really make it feel like you were missing. More like you were in that container on a 3 day trip. I guess it can fit, but it could have hinted toward it a little more. I guess he was asked where he had been, but it was more like he'd dropped off the grid. I had associated it with the container.