Desmond has flashes of Penny & Charlie during M.R.I.

At the St. Sebastian's Hospital, Desmond is being asked a series of questions by the doctor. When she asks if he's having hallucinations, he hesitates and says he's not sure if he's had hallucinations. The doctor says that his C.A.T. scan was inconclusive and she's going to send him downstairs to get an M.R.I. He objects, wanting to find Charlie, but she insists on the M.R.I.

Downstairs, the M.R.I. technician asks him if he has any keys or change, echoing what one of Widmore's men asked him before putting him into the electromagnetic box. The technician warns him that the machine will be loud and gives him earplugs. He also gives Desmond "the button," which he should push if he needs to stop the machine. Desmond seems to respond to the term "the button," possibly having a recollection of the button in the Swan Station he pressed every 108 minutes.

Once the machine starts, it seems that the electromagnetism of the M.R.I. triggers a response in Desmond causing him to see a vision Charlie's "Not Penny's Boat" message again as well as many images of Penny and his son Charlie. As he sees Penny and his son, Desmond gets emotional and suddenly starts pressing the emergency button and screams to be let out of the machine. He rips off his restraints and goes to find Charlie.

Desmond is rushed to the hospital, Eloise Hawking visits Penny

In the opening scene of "The Variable" we see Desmond being rushed into the hospital on a gurney after being shot by Ben. Penny is following the medical workers carrying little Charlie Hume. A paramedic says that he's crashing and a doctor tells Penny that she'll have to stay there and wait for news. Charlie calls out for his daddy.

Later, in the waiting room, Charlie is sleeping on a couch as Penny looks over him. Ms. Eloise Hawking slowly walks into the room and asks Penny how old her son is. Penny tells her that he's two and Eloise says that he has his father's hair. Penny says "I'm sorry, do I know you?" Eloise tells her that she knows Desmond and that it is her son's fault that Desmond was shot. Penny asks "You son is Benjamin Linus?" and Eloise replies "Good lord no" in an offended tone. Eloise then tells Penny that her son is Daniel Faraday.

It seems pretty weird that there was no visible bullet wound when Desmond was shot in "Dead is Dead" and he was able to beat the crap out of Ben, but know he's seriously wounded and crashing. It's a little thing though.

Why exactly has Eloise Hawking come to the hospital to talk to Penny? Is she really sorry for setting the events leading to Desmond being shot in motion or is this the start of an attempt to get Desmond back to the island?

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?

Desmond shows young Charlie Great Britain

Back in the present, Desmond tells young Charlie about the island of Great Britain. He appears to be at least two years old here, but it's hard to say. Penny shares her fear of her father finding out they are in the UK and tells Desmond not to underestimate him.

Penny gives birth to Charlie Hume

In the opening scene of episode three, "Jughead," we see Desmond frantically running through a market in the Phillipines looking for Efren Salonga. He finds Efran Salonga around a table with a bunch of men playing cards. It turns out that Penny is on their boat in labor and Efran Salonga is a doctor. They rush to the boat and Penny gives birth to a baby boy which we later learned that they named Charlie. It's a nice tribute to Lost's fallen hero Charlie Pace.

It's unclear when this actually takes place. It's obviously at least nine months after Penny found the survivors in the life raft.