This solution is wrong. I misunderstood the problem.

rail_fence_cipher_1.js

function railFenceCipher(operation, string, height = 3) {
  function performOperation(operation, string, height, lines) {
    let results = ''; // only for decrypt
    let currentLine = 0;
    let moveUp = true;
    let moveDown = false;
  
    for (let i = 0; i < lines[0].length; i += 1) {
      if (operation === 'encrypt') {
        lines[currentLine].splice(i, 1, string[i]);
      } else if (operation === 'decrypt') {
        results += lines[currentLine][i];
      }
  
      if ((moveUp && currentLine + 1 > height - 1) ||
          (moveDown && currentLine - 1 < 0)) {
        if (moveUp) currentLine -= 1;
        if (moveDown) currentLine += 1;
        moveUp = !moveUp;
        moveDown = !moveDown;
      } else if (moveUp) {
        currentLine += 1;
      } else if (moveDown) {
        currentLine -= 1;
      }
    }

    if (operation === 'encrypt') {
      return lines.reduce((str, line) => str += line.join(' ') + '\n', '');
    } else if (operation === 'decrypt') {
      return results;
    }
  }

  if (operation === 'encrypt' && height === 1) {
    return 'Height must be 2 or more.';
  } 

  if (operation === 'encrypt') {
    string = string.replace(/\W/g, '');
    lines = [...Array(height)].map((_, i) => i)
                .map(line => [...Array(string.length)].map((_, i) => i))
                .map(line => line.map(element => '.'));
  } else if (operation === 'decrypt') {
    string = string.replace(/\n$/, '');
    lines = string.split('\n').map(line => line.split(' '));
    height = lines.length;
  }

  return performOperation(operation, string, height, lines);
}

// each lines ends with \n
cipher = 'W . . . E . . . C . . . R . . . L . . . T . . . E\n. E . R . D . S . O . E . E . F . E . A . O . C .\n. . A . . . I . . . V . . . D . . . E . . . N . .\n';
console.log(railFenceCipher('decrypt', cipher));

// last line doesn't end with \n
cipher = 'W . . . E . . . C . . . R . . . L . . . T . . . E\n. E . R . D . S . O . E . E . F . E . A . O . C .\n. . A . . . I . . . V . . . D . . . E . . . N . .';
console.log(railFenceCipher('decrypt', cipher));

// only print letters
message = 'WE ARE DISCOVERED FLEE AT ONCE';
console.log(railFenceCipher('encrypt', message, 3));

// only encrypts print letters
message = 'WE @#$ARE      DISCOVERED -----FLEE ~~~AT ^&*(ONCE';
console.log(railFenceCipher('encrypt', message, 5));

// works with no height (3 is default)
message = 'I LOVE LAUNCH SCHOOL';
console.log(railFenceCipher('encrypt', message));

// doesn't work with height 1
message = 'I LOVE LAUNCH SCHOOL';
console.log(railFenceCipher('encrypt', message, 1));

message = 'I LOVE LAUNCH SCHOOL';
console.log(railFenceCipher('encrypt', message, 2));

message = 'I LOVE LAUNCH SCHOOL';
console.log(railFenceCipher('encrypt', message, 3));

message = 'I LOVE LAUNCH SCHOOL';
console.log(railFenceCipher('encrypt', message, 4));

message = 'I LOVE LAUNCH SCHOOL';
console.log(railFenceCipher('encrypt', message, 10));

message = 'I LOVE LAUNCH SCHOOL';
console.log(railFenceCipher('encrypt', message, 20));