Ben shoots Desmond, doesn't shoot Penny, gets beaten up by Desmond

Back at the marina, Ben stops to look at Penny on Desmond and her boat named Our Mutual Friend. Ben starts to pull his gun as he passes Desmond getting groceries from the trunk of a car. Desmond yells at Ben "Hey, what are you doing here!." Ben turns around, pulls the gun and shoots Desmond. The bullet hits the groceries and a carton of milk but as Desmond is falling to the ground, no wound can been seen on his body. Penny starts calling Desmond's name as Ben approaches and tells her not to move and "not another word."

Ben says "Hello, Penelope. My name is Benjamin Linus. I'm sorry that you're caught up in the middle of this thing, but your father" and that Penny cuts him off. She tries to explain that she and her father have relationship. Ben tells her "Your father is a really terrible human being. He's responsible for the killing of my daughter. That's why I'm here." At that moment, young Charlie Hume emerges from the boat calling for his mother. Penny tells him to go back inside and then pleads with Ben to not hurt her son. Charlie calls for his mom again and Penny yells at him to go back inside. Ben lowers his gun looking saddened by the sight of young Charlie.

At that moment, Desmond tackles Ben (though it's clearly a stunt double for Michael Emerson). Desmond beats the crap out of Ben and then pushes his body into the water. Ben is bleeding profusely and a trail of blood is left in the water.

So in this scene, we see a continuation of the humanity of Benjamin Linus. He has an attachment to children and abandons his plan to kill Penny when he sees young Charlie. Maybe because he grew-up without a mother, he didn't want Charlie have to grow-up without his mom. Could Ben's care for young kids tie into why the others took the children on the island?

Ben calls Charles to let him know he's going to kill Penny

Back off the island, Ben is walking at a marina near Los Angeles when he calls Charles Widmore. Widmore asks Ben how he got his number. Ben says that the phone number doesn't matter because he's going back to the island today. Widmore says that the island won't let him come back and that he's spent almost 20 years trying to return. Ben tells him that "Where you failed, I'm going to succeed, just as soon as I do one thing." Ben tells him that he is going to kill Penny and that he is looking at her and Desmond's boat appropriately name Our Mutual Friend (after the Dickens book Desmond plans to read). Widmore says "Don't you dare" and Ben says goodbye.

In the fourth photo you can see that Charles Widmore is standing outside of the Widmore Industries building. I just though it was worth noting.