"Why is Mark / Helly running down the hallway at the end?" Seems like they are just happy to be together. Maybe its a honeymoon of sorts because it wasn't clear what would happen to iMark after he rescued Gemma.

Helly wanted iMark to stay and iMark chose to stay because he believes he deserves a life. iMark rescued Gemma like he promised oMark he would but after that was complete he felt he'd fulfilled his promise to oMark.

When I look at iMark covered in blood it reminds me a lot of the painting we saw in S1 of the Macrodat Uprising.