Wow. Very nice job. I don't see a lot of stories written in present tense. In the rare instances where I do, they usually feel gimmicky as hell, like the author is trying to show off how clever he is. It worked very well in the context of this story though. I can't find much to criticize. Pretty much everything fits together and does what it's supposed to do. I can come up with two small niggles. The sex scene is too short. One sentence? Two words? It feels necessary to the story, but that tiny sentence feels empty. You could pace it better. Also, the fact that main character refers to his father as “Pa”. “Pa” feels too back woods and “old timey” to me, more “old timey” than World War 2.

Ugh, I had written up a long critique but accidentally clicked "home" and lost it.  So here goes from what I can remember:

An unlikely replacement has been found in San Francisco Bay.

Replacement for what?

'Swelling' is the word for the nun and her calculated effect on men.

I like what you're saying here, and it's clever, but I don't think it really fits with the rest of this paragraph.  It's a little too self-conscious, a little too "meta" or something.  It's as if you're writing about the writing, which isn't really the style of this piece.

"I don't mind you looking," 'Sister' Elaine says. "I bet it's been a while."

I don't think you should put quotes around "Sister."  Presumably the reader is going to find out very soon whether or not she's a real nun, so there's no need to prod with quotation marks as well.

Donati's crooked as a Jap's eyesight

Great period turn of phrase.  Maybe change "eyesight" to "eyes," since eyesight isn't really what's crooked?

"Well. Too well. He thinks he owns me." "I know. How'd you like to kill the bastard?" "Why?" "You always look at gift horses' teeth?" Elaine asks. "When they spring me from prison? Sure. So who's this horse's dentist?"

I really like how you did the dialog here.  It seems very natural and quick-witted, but without being so witty as to be self-conscious.  It's believable and flows very nicely.

Dean surrenders.

Brock mentioned above that he thinks that this scene is too short, but I think it's perfect as it is.  You have a good, sensual build up to the sex, it's obvious that sex is what happens, and your narrative isn't really the type to tread into more descriptive eroticism.  I think it's a good idea to leave the actual sex to the reader's imagination, because describing it in detail would add nothing to the narrative and would essentially just be filler.  So, I like it as it stands.

"Bless us, Father, for we're about to sin." Elaine smiles her lupine smile.

This seems like a one-liner from a movie or something.  Like a line they'd put up in a trailer for an action movie.

It feels like the inside of a guitar.

An interesting comparison, and I get what you're saying.  But I don't know how many other people have seen (or heard) the inside of a guitar, so this image may be lost on your readers who've never seen a real guitar (which I think is really not that far-fetched).

The connection folds up and starts to stain the floorboards.

I like this line-- good play on wood stain/blood.

I really liked this story.  You've clearly been writing for a while and have got a lot of talent.  Your action scenes are tight and dynamic, your dialog is believable and clever, and you do a very good job of setting a period atmosphere but not making it overwhelming.  On a logic note, why didn't Elaine just shoot Dean in the hotel?  Why go through this elaborate setup?  She had many chances to kill him even before they left the island.

I also like your use of the present tense.  Combined with the gritty, pseudo-noir atmosphere, I felt kind of like I was reading Sin City.  If I were you, I'd submit this to a few publications and see if you can get it published   Nice work!

Prester,

The story you've got here works, but I feel the format would work better as a screenplay. While I don't really read crime or action-adventure fiction, I felt that the prose here read exactly like screen/stage directions, and the action is predominantly dialogue driven. It's good dialogue, and I commend you for having good vision. But it seemed to me like you've got eyes of a film director... and for me something got lost in translation on the page. I am familiar with screenwriting, and once I switched into the mindset of a screenwriter, I was able to follow the action a little better. But I'm not sure if that will be the case for other readers.

"This ain't gonna work," Dean Malley says. He's standing in his boxers in a guardhouse washroom. The Catholic chaplain is getting dressed next to him. Father Donati pulls a blue prison shirt with Malley's number on it from his suitcase. The priest is a half-a-head taller than the convict and built thicker.

It's written in present tense from an omniscient POV-- which are traits of screenwriting, describing what happens on screen, with minimal emphasis on evoking the experience within a reader. What I mean is, a screenplay doesn't need to evoke the experience. The camera will do it. But in fiction, (at least the fiction I know), the author must create the experience because there is nothing to go along with the dialogue-- hence the skill of fiction, in using language to evoke a sensory experience while driving a plot.

It's the summer of 1942. The FBI is two years into prosecuting The Combination, the contract killing outfit the papers call Murder Inc. An unlikely replacement has been found in San Francisco Bay. Alcatraz has a new warden, a trustworthy gent with a very bright son. When staff members go on vacation, he doesn't scrutinize exactly who leaves the island. Donati is a cousin from one of the New York families. Doc McCullough is with the Chicago outfit, and a half-a-dozen others have their various connections. The gangsters get access to their best killers, and the warden's son gets a free ride at Stanford.

It's just explanation-- something a director would make a note of on his shooting copy of a script-- or something a producer would "pitch" to a studio executive. In my experience, it doesn't quite work in fiction.

Whitby is a guard taking at least two paychecks. He brought Dean out of the cellblock to carry the chaplain's bag. Now he's standing outside the washroom, waiting on Donati's fictional diarrhea. When the men emerge, outfits swapped, he hands Dean a pair of sunglasses. They're the big mirrored ones the Navy pilots are wearing.

We've just momentarily jumped into Whitby's POV. In fiction, 3PL POV shifting is generally not allowed. I recommend sticking with Dean and writing only what he sees, hears, feels.

Dean understands once they reach the pier. Waiting for them is a nun. No, Dean thinks. Waiting for them is a schoolboy fantasy of a nun, the nun horny adolescents dream about spending detention with. Her face is porcelain clean. Her lips are a splash of moist, violent red. Her habit clings blasphemously. The wide white collar doesn't hide her breasts. Her rosary belt rides above swelling hips. 'Swelling' is the word for the nun and her calculated effect on men.

Because we're still writing in screenplay style, I don't have a sense of character at all. I barely have gotten a sense of Dean, so when we see the word "nun" we don't really feel what Dean is experiencing. If there's greater emphasis on what Dean feels and sees, then we will see this nun who's just too hot to be a nun. But as it's written, it just seems like another character is being tossed on the page, in the hopes that the actress will bring the entrance to life.

"Elaine, Father. Sister Elaine.

I thought, what?

Dean and the nun board the launch and Donati passes over the bag and the lines are cast off and the pilot fires the engine. The boat dips and bites into the bay. Dean is staring too much and he knows it. He realizes the impropriety - maybe not before she does, but he does something about it. He turns his back, plants his elbows on the rail and looks at Alcatraz. The last of the daylight soaks the bay, capping the waves in orange and red. It's a warm red and Dean thinks about the lips he's not looking at. The island is already a hundred yards away. Lights come on. Birds wheel out from the rocks below the buildings. Dean is leaving thirty-two months before his release date.

I really think you're a natural screenwriter. This is good stuff in script for. You wouldn't even need to change anything. You know where the camera is supposed to be, and what images would evoke a good scene in a film. If you haven't ever done screen work, I'd recommend looking into it!

"I don't mind you looking," 'Sister' Elaine says. "I bet it's been a while."

Good line.

"It is fun," she says. "I like to enjoy myself. What do you want to do tonight? A show? A picture? Dinner? Dancing?"

Okay, I had to think really hard to figure out that she's not really a nun. Again, it was due to the lack of me going through the experience of what Dean's seeing.

"Well, I don't mind having fun," Elaine says. She props her elbows on the rail and stretches the way a nun never, ever would. "Before we get off the police pier a half-a-dozen cops who know Donati will see us. Having a girl won't shock them - Donati's crooked as a Jap's eyesight and everybody knows it. Either they notice he's especially shifty, and a couple inches shorter than usual, or" - she flexes her chest - "they notice what a fine new piece of trim he has."

Okay, there's a lot of fast dialogue making reference to a lot of characters and worlds outside of this boat. Since I don't know Donati or any of this other stuff, I kind of just glazed over all of this. On screen, we'd hear it. But on the page, we just skim over it.

"Can I think about it?" "Do you have to?"

Again, there's good dialogue up to this point. Well executed, polished film style.

Dean surrenders.

There should be a scene break after this.

She pinches the property

This slang will elude some readers.

She stops in the doorway, ghost-blue in the light from the window. The orange gem of the cigarette rests on her thigh.

Again, you have great vision for filmmaking. I bet you've got this scene storyboarded in your head.

In the morning, Elaine is wearing tough cotton trousers and a leather jacket over a silk blouse. Dean puts on a flannel shirt and a stiff pair of new jeans. At the airfield they board a private charter - the only way to fly without wearing khaki these days. Their clothes don't matter and they have the noisy little cabin to themselves.

Again, scene break before this paragraph.

Frank Stross and his connection are meeting at a ski resort in an old mining town. The war's savaged the resort business. It's a good place for a quiet meeting and almost as good a place for a quiet killing. Everything is prepared in advance. There's a car waiting for them when they land. Dean takes the passenger seat without protest; he hasn't driven in three years. Elaine is familiar with the area. She navigates the car through the old part of town, past wood buildings unused since the turn of the century. She stops in front of a church built of rough-hewn logs.

This is all "telly" not "showy." Let us see it through Dean's eyes, not from a camera.

He smiles back, watches her leave. He hears tires spin, hears her drive away. He scans the parking lot. It's nice arrangement. Too nice. He stands at the window for five minutes, for ten.

In my opinion, this is lazy prose.

The set-up smelled rotten even before Elaine shed her nun costume. She never said enough about the connection, and she laid out their schedule with nothing but empty space after Dean's Big Shot. That was the poison pill. If she had spy work to do, she wouldn't dangle a silly, sexy, no-strings-attached vacation in front of him.

A doublecross is happening, but I don't necessarily feel the tension or surprise.

Dean hustles down the aisle. The hymnal falls as he passes the next-to-the last pew. Elaine comes through the door, .45 in hand. Dean tangles his feet. He lets his eyes go wide and falls. His elbows hit the ground and the Springfield squirts from his grip like a floundering trout. The butt clips Elaine's knee and she falls too. He gets on top of her, grabs her gun hand and bashes it into the floorboards. She loses the pistol. Dean puts a knee on her other arm. He sits on her squirming belly and puts a forearm on her throat. Breath squeaks out, cutting off as Dean applies pressure. He holds it and sweats and Elaine goes limp. There's a pulse in her neck. She'll live.

The action is being told, but I'm not really experiencing it.

Take this all for what it's worth. In my opinion, you could ignore all of my comments, rewrite this as a screenplay and do quite well with it. But if your desire is to write it as fiction, then I hope my comments are useful. You've got a good sense of conflict and action. Some of your "shots" are very cinematic with a visual sense that I'm sure a lot of writers would love to have. I encourage you to continue developing that skill, because I can tell it comes naturally to you.

Best of luck!