I've done the End Boss twice so far, and I have a decent strategy some crewmates filled me in on.
Originally when you enter EB, you'll sit and talk to Mr. "My-Scarf-Is-Oh-So-Epic." When you're talking to him, stay out of the middle circle. As soon as the tail comes down, get out there and start beating.
Whenever your Stamina gets low while fighting the tail, sit behind it and rest up. Your crewmates can keep scratching it.
After you've spent a good while killing a tail, the Body and Arms of the End Boss will come down.
If you value your HP, do NOT kneel while the arms are still in tact. They have missiles, people. Kneeling, your damage is twice received.
Attack the left and right arms first; try not to do any damage on the body yet (it won't really have any effect yet, anyway....). Once you've freed yourself of the missile-ridden attachments, do NOT hit the Body. I stress this.
If your crew is injured or needs any kneel time or re-buff time, take it now. The Body will not attack you first until you attack it. Go ahead and run around it in circles if you want. I did that; it was actually entertaining.
The Body fires a large beam that renders you unable to move. I probably should've mentioned that earlier, but oh well. I'm too lazy to go back and change it.
One of my strategies is to stay behind the body: it won't be able to put you to "sleep" and make you unable to move, allowing you to help out your teammates if they need it.
As soon as you take the body out, get ready to dodge. If you have ghost or Fleet Feet, use them NOW.
'Animated Mines' will soon come through the northern wall, and they do target you. Run all you like. If you're too slow, they follow you. gonk
When the head comes down, just throw away any caution and start gangbeatin' it. With a full crew of 6 attacking all at once, my crew once took out the head in seven minutes flat. Just keep hitting it. xD
If anyone has anything to add onto this, go ahead and list them~!
ALSO,
What I've obtained so far:
1st Defeat: Null Fluff Plushie (Recipe)
2nd Defeat: Mechlab Robot (Recipe)
Anyone know when you get the Sinister Scarf, or is it just random ofter you've beat it a couple times?