In one of many classic scenes or images in the film, as Roger shows Townsend the photograph of the other 'Lester Townsend,' the real Townsend gasps and falls forward into Roger's arms. A knife thrown by one of the thugs - a second assassination attempt on Kaplan's life - fails. After pulling the knife out of Townsend's back, Roger is photographed holding the knife in mid-air. It appears to the crowd that Roger has killed the UN diplomat - mistaken again - but this time implicated as an assassin and murderer. (Appropriately, the man named Town-Send sends Thornhill, a typical American man-about-town, from New York out into a world of chaos.) In a panic, Thornhill must hide from both the pursuing police and enemy agents. Realizing his dilemma, he tosses the knife away and rushes out of the hall and into another cab (filmed from high above the UN, making him look like a tiny object being examined under a microscope). Now, he must attempt to clear himself of a murder he didn't commit.

In the next scene at a secret government intelligence bureau, the film audience is given more information than Roger himself knows. The viewer also has a short time-out in order to digest and hear an explanation of what has just happened in the fast-moving plot. It marks a definite transition - the violated UN building slowly dissolves to a bronze CIA plaque. In a conference room at the US Intelligence Agency (lined with world maps and a view of the Capitol), a group of agents discusses Roger's case. It is headlined on the front pages of The Evening Star with a photograph of Thornhill holding a knife and a bold headline: "DIPLOMAT SLAIN AT U.N., Assassin Eludes Police Efforts."

A photograph has been tentatively identified as that of Roger Thornhill, a Manhattan advertising executive, indicating that the name of George Kaplan which he gave to an attendant at the General Assembly Building was false - a possible motive for the slaying suggested by the discovery. And earlier today Thornhill had appeared at a Glen Cove Long Island police court and charged with drunk driving with a stolen car. In his defense, he charged that the murder victim, Mr. Townsend had tried to kill him the night before.

As intelligence representatives, they know that Kaplan is an imaginary, fictional agent who "doesn't even exist" - he was devised as a fictitious decoy to mislead foreign spies (and smugglers) such as Philip Vandamm from discovering the identities of real agents. And apparently, Thornhill is an innocent man who has been mistaken for the non-existent agent. He is:

...the poor sucker (who) got mistaken for George Kaplan...Vandamm's men must have grabbed him, tried to put him away using Lester Townsend's house - and the unsuspecting Mr. Townsend winds up with a stray knife in his back. C'est la guerre.

One of the agent's reactions summarizes the film's entire tone and mood:

It's so horribly sad. How is it I feel like laughing?

The intelligence agency chief, a paternalistic official named the Professor (Leo G. Carroll), suggests that they do nothing and take advantage of their "good fortune" by using Thornhill as a decoy. [The Professor's character may have been modeled after John Foster Dulles, the notable Secretary of State under Eisenhower, and after Dulles' brother, the head of the CIA at approximately the same time.] He decides that Thornhill should be left to defend himself - saving Thornhill would only interrupt their counter-espionage tactics and endanger their "own agent" - a soon-to-be introduced film character:

We do nothing...That's right, nothing. Oh, we could congratulate ourselves on a marvelous stroke of good fortune. Our non-existent decoy George Kaplan created to divert suspicion from our actual agent has fortituously become a live decoy... What can we do to save him, without endangering our own agent?...We didn't invent our non-existent man and give him the name of George Kaplan, establish elaborate behavior patterns for him, move his prop belongings in and out of hotel rooms for our own private amusement. We created George Kaplan and labored successfully to convince Vandamm that this was our own agent hot on his trail for a desperately important reason...If we make the slightest move to suggest that there is no such agent as George Kaplan, give any hint to Vandamm that he's pursuing a decoy instead of our own agent, then our agent working right under Vandamm's very nose will immediately face suspicion, exposure and assassination, like the two others who went before.

Therefore, the "callous" group concludes that Thornhill use his own resources without any of the protections of civilization. In an overhead shot, the only woman in the group, Mrs. Finlay, expresses sympathy for Thornhill's plight and doom:

Good-bye, Mr. Thornhill, wherever you are.

Police and detectives search for Roger Thornhill in a crowded Grand Central Station in New York. [This scene echoes the opening scene when Thornhill was again surrounded by crowds.] He sits in a phone booth talking to his mother to tell her that he is leaving New York by train. His plan is to board the Twentieth Century Limited to Chicago. Having learned from the Plaza Hotel that Kaplan checked out and is headed for the Hotel Ambassador East in Chicago, his immediate goal is to search for Kaplan and discover the man's identity so he can clear his own name and solve his dilemma. In his phone conversation, he foreshadows the famous crop-dusting sequence when he is subjected to his enemies outside a plane:

The train, it's safer...Well, because there's no place to hide on a plane if anyone should recognize me...oh, you want me to jump off a moving plane?

Noticing a man reading a newspaper with the headlines of a search for the assassin ("MANHUNT ON FOR U.N. KILLER"), Roger dons sunglasses but is recognized when trying to buy a train ticket. He bluffs his way past the ticket gate and onto the train, where he first bumps into an icy cool, platinum blonde Eve Kendall (Eva Marie Saint) in the corridor. As he momentarily ducks into a compartment, the obliging lady helps him evade and mislead the police. He mentions that "seven parking tickets" are the reason for his flight from authorities. Later, he evades ticket takers by hiding in the train's toilet, and then finds himself seated across the table from the same blonde woman in the dining car. Nervously looking around, he orders dinner and asks for advice:

Roger: Do you recommend anything?
Eve: The brook trout. A little trouty but quite good.

She appears to know all about him - he looks "vaguely familiar" and she honestly believes he has a "nice face."

Roger: Oh, you're that type.
Eve: What type?
Roger: Honest.
Eve: Not really.
Roger: Good, because honest women frighten me.
Eve: Why?
Roger: I don't know. Somehow they seem to put me at a disadvantage.
Eve: Because you're not honest with them?
Roger: Exactly.

And so begins a long series of seduction scenes during their cross-crountry train ride between a mysterious, ambiguous, baffling woman and a handsome ad executive - unattached and on the make. She is particularly appealing with personal traits of attractiveness and worldliness that match:

Roger: What I mean is, the moment I meet an attractive woman, I have to start pretending I have no desire to make love to her.
Eve: What makes you think you have to conceal it?
Roger: She might find the idea objectionable.
Eve: Then again, she might not.
Roger: Think how lucky I am to have been seated here.
Eve: (ironically) Well, luck had nothing to do with it.
Roger: Fate?
Eve: I tipped the steward $5 dollars to seat you here if you should come in.
Roger: Is that a proposition?
Eve: I never discuss love on an empty stomach. [She actually says, "I never make love on an empty stomach," but the line was dubbed over.]
Roger: You've already eaten.
Eve: But you haven't.

Then, she formally introduces herself to him - and then shocks him by admitting that she knows exactly who he is and what he's wanted for. She is also suggestively amorous and unopposed to making love to him:

Eve: I'm Eve Kendall. I'm twenty-six and unmarried. Now you know everything.
Roger: Tell me. What do you do besides lure men to their doom on the Twentieth Century Limited?
Eve: I'm an industrial designer.
Roger: Jack Phillips. Western sales manager for Kingby Electronics.
Eve: No, you're not. You're Roger Thornhill of Madison Avenue, and you're wanted for murder on every front page in America, and don't be so modest.
Roger: Whoops!
Eve: Oh, don't worry, I won't say a word.
Roger: How come?
Eve: I told you. It's a nice face.
Roger: Is that the only reason?
Eve: It's going to be a long night.
Roger: True.
Eve: And I don't particularly like the book I've started.
Roger: Ahhh.
Eve: You know what I mean?
Roger: Uh, let me think. (Pause) Yes, I know exactly what you mean...

She suggests by her flirtations that she likes him and may be willing to hide him in her compartment. She notices his personalized matchbook with initials "R O T" when he lights her cigarette. As he himself admits, the O stands for nothing - the 'zero' and hollow quality of his life with no commitments or causes - in a world of 'false' advertising. [An inside joke, Hitchcock's former producer boss, David O. Selznick, had a middle initial of 'O' that also stood for nothing.]

Eve: Roger O. Thornhill. What does the 'O' stand for?
Roger (shrugs): Nothing. (He lights her cigarette) I'd invite you to my bedroom if I had a bedroom.

She sensuously caresses his hand, blows out the match. He coyly mentions that he has "no place to sleep," so she invites him to share her large "easy-to-remember" drawing room (Room E, Car 3901 - a Hitchcockian self-reference to his earlier film, The 39 Steps (1935)) all to herself. Noticing that the train has stopped and that several policemen are boarding the train, she warns him:

Eve: Incidentally, I wouldn't order any dessert if I were you.
Roger: (eagerly) I get the message.
Eve: That isn't exactly what I meant. This train seems to be making an unscheduled stop, and I just saw two men get out of a police car as we pulled into the station. They weren't smiling.

After following her to her train compartment, Roger hides in the closed upper bunk like a sardine as the state police search the train and stop at her door to question her about the stranger she sat with at dinner. She appears surprised when told the fugitive is wanted for murder, thinking it odd that their dinner conversation was "rather innocuous I must say considering he was a fugitive from justice." After they leave, she releases the upper bunk so he can breathe. He questions why she covered for him:

Roger: Tell me, why are you so good to me?
Eve (flirting): Shall I climb up and tell you why?

At the start of a lengthy, sizzling romantic scene, she offers to have him stay in her hotel room in Chicago while she contacts Kaplan for him to arrange for a meeting. Thornhill suggests that it may be too dangerous, but she encourages him in a playful manner to kiss her. She surrenders entirely to his hands around her head (is he positioning himself to throttle her or strangle her?):

Eve: I'm a big girl.
Roger: Yeah, and in all the right places too. (They share a lingering kiss.)
Eve: You know, this is ridiculous, you know that don't you?
Roger: Yesss.
Eve: I mean, we've hardly met.
Roger: That's right.
Eve: How do I know you aren't a murderer?
Roger: You don't.
Eve: Maybe you're planning to murder me right here tonight?
Roger: Shall I?
Eve: Please do. (Another long kiss.)
Roger: Beats flying, doesn't it?
Eve: We should stop.
Roger: Immediately.
Eve: I want to know more about you.
Roger: What more could you know?
Eve: You're an advertising man, that's all I know.
Roger: That's right. (They shift positions.) The train's a little unsteady.
Eve: Who isn't?
Roger: What else do you know?
Eve: You've got taste in clothes, taste in food...
Roger: ...and taste in women. I like your flavor.
Eve: You're very clever with words. You can probably make them do anything for you. Sell people things they don't need. Make women who don't know you fall in love with you.
Roger: I'm beginning to think I'm underpaid.

A porter interrupts their seduction, but they soon continue when he leaves:

Roger: Now where were we?
Eve: Here. (They kiss again passionately.)
Roger: Yes. Nice of you to have opened the bed.
Eve: Yes.
Roger: Only one bed.
Eve: Yes.
Roger: That's a good omen, don't you think?
Eve: Wonderful.
Roger: You know what that means?
Eve: Hmmm.
Roger: What? Tell me.
Eve (in a bow to censors): It means you're going to sleep on the floor.

Although Eve is willing to have a one-night stand, she also yearns for involvement with him and has begun to fall in love (against her will) - below the surface. However, she is also deeply troubled and ensnared. She slips a note to the porter, who delivers her message to another compartment: "A message from the lady in 3901." The handwritten message is read by an unseen individual:

What do I do with him in the morning? Eve.

[Soon, we learn the nearby sleeping car room is occupied by Leonard and the fake 'Townsend' (Vandamm).]