Definitely one of the most difficult SGA episodes to handle and comprehend…
Some spoilers if you continue…
On the surface, the plot is rather simple. Henry Wallace heads a company that is developing "alien technology" for commercial use on Earth. He has some nanites developed as a result of research in the Pegasus Galaxy. He even has the basic "replicator program" for these nanites. He's very much aware of Star Gate Command and Dr. Rodney Mc McKay's work with the nanites and the underlying programming of them. He has injected these nanites in his daughter (who is suffering from leukemia) but his programmers can't make them work. He's monitoring email traffic and when Rodney contacts his sister, Jeannie (introduced in Season 3: McKay and Mrs. Miller), Wallace has her kidnapped. This prompts Rodney (along with Sheppard and Ronon) to return to Earth where upon Rodney is also promptly kidnapped.
Wallace tells McKay and Jeannie that he'll free them if they can get the nanites to heal his daughter. Jeannie is inclined to do this but McKay wants to escape. The escape attempt fails and Wallace injects nanites into Jeannie to motivate them to complete the program. They basically remove the nanite restrictions and let them do what they are supposed to do. The young girl recovers. However, she soon has heart failure and dies. Shortly thereafter though, she revives. It turns out she had a heart problem and the nanites decided to fix that by shutting down her heart. This, of course, causes brain damage which the nanites repair but can't bring back her memories and/or etc. She is "blank slate."
Enter Sheppard and Ronan to the rescue. The race is now on to reprogram the nanites in Jeannie since she has epilepsy and they might also shut her brain down. They break her legs to give the nanites something to do but McKay can't do the reprogramming. So, they bring Todd (the Wraith) to Earth to help out. But, he's too week from hunger so Sheppard turns to Wallace to sacrifice himself to Todd so he can complete the reprogramming and save Jeannie.
Ethical problem #1: One of the primary goals of our heroes is to prevent the Wraith from getting to Earth. Yet, they bring one here. This shocked and concerned a lot of viewers. And, without question, this is a deviation from our heroes' directive and morals.
Ethical problem #2: Another goal of our heroes is to prevent Wraith from feeding on humans. Yet here, Sheppard arranges for a Wraith to feed on a human. He does so in such a way that it can only be called "assisted suicide by Wraith." He also says the report will indicate that it was accident and the Wraith attacked Wallace while on a tour meaning he's going to falsify the whole thing. There's no question this is totally out of context of what we know about Sheppard and what we expect from our SGA heroes.
The clue maybe found in the episode title. "Miller's Crossing" was an early '90's Coen brother's film. It was all about a mythical place where two crime syndicates were battling each other. Usual "social morals" were completely absent and everyone established their own ethics. Nevertheless, even those ethics could be changed based on someone else changing their ethics.
In this case, it was Wallace who changed the ethics first which led to Sheppard changing his ethics. I would not recommend this for people who want SGA to stay in single ethical/moral bent. The ethical switch is simply too radical for some to accept. For myself, I appreciate what the story is trying to do but really would like to live in a continual fantasy that our heroes are always going to be above this sort of thing.