A red letter from JJ and codes abound.
There is a message on the back though to be found.

Binary and morse code - this is a simple translator,
but first - the message on the back - use these codes later.
"...Start with scans" the note suggests.
Scan three QR codes to helps JJ with his requests.

This Emergency Protocol letter serves as a translation key for binary and morse code, which will be used later, but for now take note of the clue on the back that suggests starting with the scans. Find the item in your envelope with 3 ships and scan each of the QR codes.

Scan each QR to find three words - that seems strange.
Now make one word - you'll need to combine and rearrange.

"voices + rant + on" are your clues here.
Combine and rearrange to make it clear.
The answer involves talking - you’re oh so near!

In each of the three pictures there is a hidden word in the image “voices" "rant" and "on”. Use these three words to combine and rearrange them like an anagram to make a single word. There are only two possible options in the english language, with the correct answer being CONVERSATION. Enter this word into the portal and advance.

If you stay true to JJ’s course,
you’ll note the cities and then the Morse.

Listen for a list of places. Use that order to fill in the spaces.
The password next he will endorse. Listen for the code in Morse.

JJ mentions locations that match your ticker tape.
Put them in order-and use binary-to help JJ escape.
Four short beeps make an "H" - one short and one long make an "A".
Now listen for two more letters - what is JJ trying to say?

To find the username, go to 2:30 in the video feed from JJ and you will hear him tap a string of Morse code to you. Use the red "Emergency Protocol" slip to translate the corresponding Morse Code:
H = . . . .
A = . _
C = _ . _ .
K = _ . _

Use HACK as your username.

At 2:48 in the video signal from JJ he names cities that he has been to:

1. Paris (CDG)
2. Tokyo (HND)
3. Dubai (DXB)
4. Lagos (LOS)
5. London (YXU)
6. Buenos Aires (EZE)
7. New York (JFK)

This list of cities corresponds to each of the cities listed on the ticker tape strip.
Rearrange the cities to match the order mentioned by JJ, then use the red "Emergency Protocol" slip to translate the corresponding binary numbers 2867513 this is your password for the submarine's network.

Hit submit and continue.

Looking closely you will see,
a name that starts with the letter V.

Tilt your head a bit and maybe lean.
Looks like it's upside down - that's just mean.
You’ll need the name for the next screen.

There is a name written upside down on the doppler:VICTOR.
Use this as the password for the next screen. Having trouble seeing it? Here are the letters outlined.

A sonar puzzle you will have to learn,
you must cut it first and then you can turn.

Many lines you can combine,
but try it first with a specific line.
See what your cousin sees,
and point the arrow to 15 degrees

15 degrees, and a unique underline - thin, thick, thin.
Rearrange the sonar to align - and in the centre place the pin.
Point the arm to 15 and three sets of numbers are revealed.
Surely, a password this must yield.

Cut out the rings of the sonar puzzle where you see the scissor icons. Note on the console JJ shows you that "15 Degrees" is underlined with a thin-thick-thin line combination. You will notice the same thin-thick-thin line combination on each of the three rings of the black and green sheet. Align the three rings so that this line combination aligns. Fasten the clear plastic arm to the centre of the sonar and point it at 15 degrees. The sets of numbers are revealed through the holes of the sonar arm 17, 274 and 115. Combine these numbers to make 17274115 which is your heading code for the next step. See here for an example image.

8, 3 and 6? What is this mission?
Count not the value, but instead, the position.

The order of the lights are saying something - you're not crazy.
Match the numbers on the card, you see.

Wait for a pause in the blinking lights, then begin to count.
Note the 8th, 3rd, and 6th and this code you shall surmount.

If you pay attention to only the 8th, 3rd and 6th flashing light, it spells out the word CANCEL. That is your password to disable the auto-pilot.

Four sets of grids you did find,
and the wallet photo - did you look behind?

When the woman turns her back to you,
she reveals the numbers you must use.
Employ the grids to mark and plot,
and find a word spelled with many a spot.

Set four grids side by side just like JJ's screen.
Label the axis with the letters and numbers that are green.
On the back of the wallet photo - coordinates you have seen.

Align the four grids provided to match the four grids seen on JJ's screen (medium size, Large, large, small). Label them as depicted. Then, plot the coordinates from the back of the wallet photo onto the four grids. When finished you will discover the word FREEDOM as seen here. This is your final password to help JJ escape the Hunter's submarine.