cipher - A mysterious email from Ryanair

You are a secret agent in the service of the KGB, and after a setback when the higher-ups thought your cover had been blown, you have embarked on a highly dangerous mission to infiltrate MI6. Under the pseudonym of Flynn Smith, you are working undercover in London when you receive the following mysterious email.

From: "itinerary@ryanair.com" < itinerary@ryanair.com >
Sent: Wed, 13 May 2015 10:27AM +0400
To: ██████████████████████
Subject: Ryanair Travel Itinerary

Dear Mr Smith,

THANK YOU FOR BOOKING WITH RYANAIR.
THIS IS YOUR BOOKING CONFIRMATION, PASSENGER ITINERARY AND RECEIPT EMAIL. PLEASE CHECK YOUR FLIGHT(S) AND PASSENGER(S) DETAILS BELOW.

MSYSTLMSPORDSTLTPA RYGMUCZAGBUDHEM ADADMEIKAUFA KBLTSEKTMURC XNNDACRGNLPFXNN CGKPERDRWADLBNE

DO NOT REPLY TO THIS EMAIL.
_{Copyright 2014 Ryanair Ltd. All rights reserved. Cheap Flights - Lowest European Fares, Low Cost Airline.}

You are confused: with all your expenses paid by the intelligence service, you never fly with a budget airline company like Ryanair. Perhaps they've got you mixed up with another Mr Smith - but how come your email address is on their records? Also there aren't even any ticket details in the email, only a nonsensical string of letters. The message must have been garbled.

But remembering your previous experience of an apparently spam email, you examine it more closely, wondering if there's a message hidden within it. After several minutes at your computer, you find the hidden message and your eyes widen. You reach for the drawer in which your handgun is stowed; you're in danger!

Looking even more closely, you realise that there's a second message hidden within the more obvious one. Your KGB agent handler is telling you where you must go - and probably also that you're in danger. It seems as though everything's under control, but you must move fast.

What is the hidden message?

Answer

Excellent puzzle! The secret message is

RUN NOW

Here's how I solved it...

Since the email seems to refer to a flight itinerary, I discovered that the code words must actually consist of three-letter airport abbreviations:

MSY = New Orleans, Louisiana
STL = St. Louis, Missouri
MSP = Minneapolis-Saint Paul, Minnesota
ORD = Chicago, Illinois
STL = St. Louis, Missouri
TPA = Tampa, Florida

RYG = Rygge, Norway

MUC = Munich, Germany
ZAG = Zagreb, Croatia
BUD = Budapest, Hungary
HEM = Helsinki, Finland

ADA = Adana, Turkey
DME = Moscow, Russia
IKA = Tehran, Iran
UFA = Ufa, Bashkortostan, Russia

KBL = Kabul, Afghanistan
TSE = Astana, Kazakhstan
KTM = Kathmandu, Nepal
URC = Ürümqi, Xinjiang, China

XNN = Xining, Qinghai, China

DAC = Dhaka, Bangladesh
RGN = Yangon, Myanmar
LPF = Liupanshui, Guizhou
XNN = Xining, Qinghai, China

CGK = Jakarta, Indonesia
PER = Perth, Australia
DRW = Darwin, Australia
ADL = Adelaide, Australia
BNE = Brisbane, Australia

And with a bit of Googling and doodling, I ended up with this: