Oh fun. This is actually a set I can counter with something I like.
Naviathan @ Leftovers
Ability: Heatproof
EVs: 252 HP / 4 Def / 252 SpD
Calm Nature
- Calm Mind
- Slack Off
- Substitute
- Scald
Counter
This Naviathan set takes incredibly little from anything this Greninja can do, and can proceed to set up in its face. Very little to say here. Heck, even Ice Beam can't win it with a lucky freeze due to Scald auto thawing. I mean, I guess there is the ~.00001% chance it flinches with Extrasensory 6-8 times in a row, but.... yeah....
Anyways though, as far as the whole point on the mon needing to actually be useful, well, this is actually a Naviathan set I like quite a lot. In general, this set is far more about taking on walls than sweepers. It just so happens that it works out against this Greninja. However, its true goal it to get in on a wall, and get up a sub and start setting up on it until it cannot be stopped. This kind of Naviathan set is one of its two main kinds, and while a lot of people prefer either a second attack or Taunt, I personally find Substitute to work well, as it protects you from both direct status moves as well as secondary effects and the weaker damage things will be throwing at you. One thing you might question with this set is the choice of a specially bulky EV spread instead of a physically bulky one on something that is going to be setting up Calm Minds, but I actually find that the specially bulky spread works out quite well. Naviathan's physical bulk is quite respectable, invested or not, while the special bulk is not so much. And ultimately, its goal is to be taking on special attackers and walls who do not hit that hard physically anyways. But the main thing that initially attracted me to the specially defensive set is Cyclohm. On a physical set, Defensive Clohm can come in and pretty much ruin your day. While you could survive two Discharges after a Calm Mind, the amount of damage it does far outstrips what you can do, and the threat of paralysis could ruin your day. But on a specially bulky set, you only ever need to risk that once. After 2 CMs, there is a very high chance Clohm cannot break your subs, meaning it becomes fodder for you, which is very nice when you want to take on bulky teams where Clohm can appear.
252 SpA Life Orb Protean Greninja Extrasensory vs. 252 HP / 252 SpD Naviathan: 74-88 (18 - 21.4%) -- possible 7HKO after Leftovers recovery
0 SpA Naviathan Scald vs. 0 HP / 0- SpD Greninja: 60-72 (21 - 25.2%) -- 0.1% chance to 4HKO