EDIE: But Pop, I've seen things that I know are so wrong. Now how can I go back to school and keep my mind on... on things that are just in books, that aren't people living?
Edie told Father Barry not to hide in the church—to get out in the world. Here, Edie faces the same choice. She can't go back to school, since she's realized she needs to search for justice and truth in the world.
BARRY: Isn't it simple as one, two, three? One, the working conditions are bad. Two, they're bad because the mob does the hiring. And three, the only way we can break the mob is to stop letting them get away with murder.
Barry's right—it is that simple. What's not simple is finding the courage to actually take the third step. Especially because people who take the third step, like Joey and Dugan, keep getting killed.
BARRY: There's one thing we've got in this country and that's ways of fightin' back. Gettin' the facts to the public. Testifyin' for what you know is right against what you know is wrong. Now what's ratting to them is telling the truth for you. Now can't you see that? Can't you see that?
Barry has to get the longshoremen to stop letting the gangsters determine what justice is (e.g. killing snitches). They need to adopt a higher morality.
BARRY: Some people think the Crucifixion only took place on Calvary. They better wise up! Taking Joey Doyle's life to stop him from testifying is a crucifixion. And dropping a sling on Kayo Dugan because he was ready to spill his guts tomorrow, that's a crucifixion. And every time the Mob puts the pressure on a good man, tries to stop him from doing his duty as a citizen, it's a crucifixion. And anybody who sits around and lets it happen, keeps silent about something he knows that happened, shares the guilt of it just as much as the Roman soldier who pierced the flesh of our Lord to see if he was dead... Boys, this is my church! And if you don't think Christ is down here on the waterfront, you've got another guess coming!
In Barry's eyes, any act of injustice against the innocent is a version of the crucifixion. But, if no one stands up, it doesn't become a moment of redemption—the bad guys continue to thrive.
BARRY: Every morning when the hiring boss blows his whistle, Jesus stands alongside you in the shape-up. He sees why some of you get picked and some of you get passed over. He sees the family men worrying about getting the rent and getting food in the house for the wife and the kids. He sees you selling your souls to the mob for a day's pay...And what does Christ think of the easy-money boys who do none of the work and take all of the gravy? And how does he feel about the fellows who wear hundred-and-fifty dollar suits and diamond rings, on your union dues and your kickback money? And how does He, who spoke up without fear against every evil, feel about your silence? You want to know what's wrong with our waterfront? It's the love of a lousy buck. It's making the love of the lousy buck - the cushy job - more important than the love of man! It's forgettin' that every fellow down here is your brother in Christ!
The gang's philosophy is based on money and power—it's basically the opposite of Barry's Christianity, where love and justice are the main things.
BARRY: But remember, Christ is always with you - Christ is in the shape up. He's in the hatch. He's in the union hall. He's kneeling right here beside Dugan. And He's saying with all of you, if you do it to the least of mine, you do it to me! And what they did to Joey, and what they did to Dugan, they're doing to you. And you. You. ALL OF YOU. And only you, only you with God's help, have the power to knock 'em out for good.
If Christ is always present with everyone, no one can justify being totally self-centered or doing something awful to someone else. They have to recognize that they're connected through Christ and have moral obligations to each other.
LAWYER: Would you say that Mr. Friendly made it clear to you it was absolutely necessary he murder Joey Doyle in order to maintain his control on the docks of the waterfront locals? Is that correct?
Terry answers, "Yes" to this question, even though we don't actually see the moment of truth. It's the most crucial point in the movie, when Terry gives up his old understanding of morality (e.g. being against snitching) and embraces his new understanding—bringing justice to a murderer and protecting the innocent.