Some of the best Nip/Tuck episodes feature a McNamara/Troy patient whose crisis parallels everybody else's personal crises. This episode is one of the more obvious examples of this, with a central storyline that is mirrored in the actions every member of the main cast commits.
The Agatha Ripp storyline kept you guessing right until the end. It's unfortunate to say it, but these types of cover-ups and deception happen every day in various religions, with people like Sister Rita-Claire using disturbed and abandoned people like Agatha to reap their own rewards. Sarah Paulson was a great guest star, and genuinely convinced the audience of her character's stigmata, even if it turned out in the end that it was lies all along.
Faith and believe also bled into everybody else's subplots. I loved how Liz's doctor summed up motherhood and pregnancy as "trusting in the unknowable", which struck parallels with religion as a whole. It takes a strong (or a weak, some may say) person to trust in something that hasn't actually been proved, and I thought Ryan Murphy put that message across in a great way.
A lot of weight was put on the Bible passage about "false prophets" and how people you trust could be revealed to be nothing but "ferocious wolves", which ended up affecting Sean in a greater way than he originally thought possible. Julia was plagued by something visually similar to stigmata, when her own guilt over Matt's paternity caused wounds and bruising to appear across her stomach. Eventually confessing to Sean that Christian is Matt's father, Sean discovered the passage came true in some ways, with his best friend becoming that "ferocious wolf" of the verse.
An excellently written episode and one that manages to not patronize the audience, which is something that could easily have occurred in the hands of a lesser writer.