Edit in JSFiddle

const flights = [
  ['B', 'C'],
  ['E', 'F'],
  ['C', 'D'],
  ['D', 'E'],
  ['A', 'B'],
];

const findRoute = flights => {
	let sources = [];
  let destinations = [];
  
	flights.forEach((flight, index) => {
  	sources.push(flight[0]);
    destinations.push(flight[1]);
  });
  
  let sourceCity = sources.filter(source => !destinations.includes(source))[0];
  let destinationCity = destinations.filter(destination => !sources.includes(destination))[0];
      
  document.write(`Origin: ${sourceCity}<br>Destination: ${destinationCity}`);
};

findRoute(flights);