[quote=@yoshua171]
[@Fallenreaper] Kk. Not sure how she can stop Dune Hunter. After the puppet is underwater.
[/quote]

The main issue, should've addressed this originally, is if she could see him either speeding toward the ship or have slipped underwater. 

Ideas I have, unless all are impossible are as listed below, though using stop wasn't the best choice of words. Let me replace it with the words: slow he down, instead.  

[list]
[*]Using her Hidden Mine Technique, she can attach it to a kunai or shuriken. Then toss at an angle where the puppet is ramming into the ship. It might not stop him but it could slow his speed down enough to allow the ship not to be sank. 
[*]End up using Thunderbolt or Electromagnetic Murder (I'm leaning to this one) and hit the water, using it as a magnifying agent due to it being water. Now it might weaken due to being spread, but it would still hit him and possibly slowly him down. I'll have to research Sea water and how it reacts with electrical currents though, namely to make sure the salt doesn't prevent anything or create issues. 
[*]Last option is likely to use Landmine to create a wave that would end up at least altering the ship's position or possibly slowing DH down.[/list] 

I'm honestly hoping one of these are least plausible.