The majority of this episode focuses on McNulty and his newly cooked up scheme to bring down Marlo by tampering with evidence and the body of a dead homeless person so that it looks like a serial killer did it. Even though one can see that this may be the only way for the department to refocus on Marlo and his crew, it definitely represents a moral issue; especially with Bunk who wants nothing to do with it.
At the newspaper, the head office in Chicago, for financial reasons, needs to shrink its staff and close down many international bureaus. The staff constantly hears, "We must do more with less". But as is implied throughout this season so far, one does less with less not more. Many employees are being forcibly bought out of their contracts. Real stories like the one that Alma Gutierrez wrote about involving the 3 people killed in their home, got butchered and buried, because as Fletcher said "Wrong Zip Code. They're dead where it doesn't count."
And finally Omar shows his face at the end, realizing that he needs to come out of hiding and back to Baltimore because his friend and confidant Butchie just got killed by Marlo's crew.