Moves
Ice Beam is Greninja's main tool of assassination, allowing Greninja to OHKO most Pokemon 4x weak to Ice, KO physically defensive Hippowdon, and have a 68% chance of OHKOing Zapdos. While Dark Pulse doesn't hit as many targets super effectively, it allows Greninja to 2HKO Cresselia and Aegislash (though you should watch out for Weakness Policy) and OHKO Mega Gengar. Greninja might have a low Attack stat, but Gunk Shot makes Greninja an effective mixed attacker. It OHKOes Azumarill and Sylveon and 2HKOes offensive Rotom-W, Pokemon that would otherwise counter Greninja. Because Greninja also survives a Belly Drum-boosted Aqua Jet at full health, it can be an effective emergency check to Belly Drum Azumarill. Gunk Shot also gives Greninja a Fighting resistance, meaning that users of Mach Punch and Vacuum Wave can no longer check Greninja.
The final moveslot depends heavily on what you need Greninja to cover for your team. Low Kick rounds out the set well, doing at least 79% to minimum HP Mega Kangaskhan. It also allows Greninja to OHKO Tyranitar and Bisharp and 2HKO specially defensive Ferrothorn. If you're more worried about Suicune, Grass Knot is an effective way to stop it from setting up, with Grass Knot even having a chance to 2HKO Suicune after it has used Calm Mind once. As a bonus, it will also still 2HKO Tyranitar. Grass Knot does laughable damage to the lightweight Rotom-W, though, so if you care to do more damage to Rotom-W, you can use Hidden Power Grass at the cost of being able to beat Suicune. Water Shuriken might seem like a strange choice, as Greninja is already extremely fast. However, it allows Greninja to snipe Blaziken and Talonflame when they are around half their health (which is especially useful because it means Talonflame will be OHKOed after Stealth Rock damage). Water Shuriken will also prevent Pokemon with Fighting-type priority from OHKOing Greninja before it does anything, allowing Greninja to deal some damage before it gets KOed. If your team needs some extra firepower, consider Hydro Pump. Hydro Pump is Greninja's most powerful weapon, OHKOing Heatran and dealing over 70% to the troublesome Mega Mawile, which Greninja will lose to otherwise. If you're paranoid about Hydro Pump's accuracy and don't mind missing out on the OHKO on Heatran, Surf can be used as a reliable move to 2HKO Mega Mawile, while Scald is slightly less powerful in exchange for a burn rate.
If you want a move that can hit both Mega Mawile and Ferrothorn, Hidden Power Fire is also a good option, doing the most to Mega Mawile out of Greninja's tools and OHKOing Scizor and physically defensive Ferrothorn. If Mega Venusaur is a huge problem for your team, Extrasensory can be used to 2HKO it while protecting Greninja from Fighting-type priority. Finally, while U-turn doesn't offer any compelling coverage, it can allow Greninja to be more useful early in the game by giving Greninja the ability to scout the Pokemon your opponent has chosen and perform well against some leads such as Focus Sash Garchomp. One final thing to note about Greninja's complicated move choices: if your team can adequately handle Azumarill, you can elect to replace Gunk Shot with any of the moves listed above.
Set Details
Greninja should always run maximum Speed to avoid KOs. Additionally, this Greninja should not be leaving the dojo without a Life Orb, because the extra power is necessary to vanquish many foes in the Battle Spot Singles battlefield. With a Naive nature and 20 Attack EVs, Greninja OHKOes Azumarill with Gunk Shot, and the rest of the 236 EVs go into Special Attack for maximum revenge killing power. If for any reason you decide to make your Greninja a full special attacker, run a Timid nature with maximum Special Attack.
If you plan on running Hidden Power Fire, use an EV spread of 20 Atk / 240 SpA / 248 Spe, because due to Pokemon being level 50 in this metagame, any extra EVs in Special Attack and Speed would be a waste when the Pokemon is forced to have an IV of 30. Finally, an interesting option to consider is to hone Greninja's martial arts skill by running maximum Attack EVs. This gives the ninja frog a 93% chance to OHKO minimum HP Mega Kangaskhan with Low Kick and a guaranteed OHKO on maximum HP Heatran. Ice Beam will still KO all the targets 4x weak to it, but unfortunately, Dark Pulse will lose the guaranteed 2HKO on Cresselia and the OHKO on Mega Gengar and Mega Slowbro.
Usage Tips
It's best to keep Greninja hidden in the shadows early in the game; Greninja's defenses leave it OHKOed by many of Battle Spot Singles's powerful offensive Pokemon. Getting Greninja in after a KO is usually the best way for it to enter the battle, and letting Greninja take the stage later in the game when your opponent's team is weary from battle can lead to a clean sweep.
If using Greninja earlier in the game, try to get it in on something it can easily scare out and revenge kill. Pokemon that are weak to Ice such as Garchomp, Mega Salamence, and Zapdos are great candidates for Greninja's assaults. It might seem like a good idea to use Greninja early in the game, but think carefully before you do this: Greninja can't handle any leads that run Focus Sash or powerful priority moves. If using U-turn, Greninja can handle the lead position more comfortably by U-turning slower Focus Sash Pokemon that lack priority, such as Garchomp.
Finally, because Greninja's mere presence can force switches, you can employ the high-risk, high-reward tactic of double switching, which can give your team an edge against defensive switch-ins such as Porygon2 and Suicune.
Team Options
The greatest support Greninja's comrades can give it is residual damage. Wearing down the opponent's team can transform Greninja from a simple revenge killer to a terrifying cleaner. The easiest way to support Greninja is to use Pokemon wearing a Rocky Helmet or ones with a contact-damaging ability. Pokemon such as Garchomp, Cresselia, and Zapdos work well here. A big bonus is that Mega Kangaskhan will fall to Greninja after only one round of Rocky Helmet damage.
Greninja also appreciates sandstorm support from Tyranitar and Hippowdon. Tyranitar and Mega Tyranitar share an unfortunate Mach Punch weaknesses with Greninja, but they can effectively switch into Talonflame and also set up on Porygon2 with Taunt and Dragon Dance. Hippowdon, on the other hand, can defeat troublesome, physically based revenge killers such as Blaziken and Choice Scarf Garchomp. Just note that Sand Stream support is a double-edged katana, as Life Orb and sandstorm damage can wear Greninja down to the KO range of priority attacks. The final form of residual damage support is Stealth Rock, which, while difficult to set up, can be especially effective with Greninja, as Stealth Rock puts Talonflame into the KO range of Water Shuriken.
There are some troublesome foes that must be taken into account when hiring Greninja for your team. Porygon2 is near the top of the list, as it is able to effortlessly wall Greninja and either blast the ninja with Tri Attack or destroy its Speed with Thunder Wave. If Greninja isn't running the right moves for it, Mega Mawile will become a terrifying force to face, while Mega Venusaur can use Greninja as an opportunity to stall with Leech Seed. Finally, fast Fighting-type attacks and Talonflame can bypass Greninja's Speed and assassinate it. Mega Gengar is an excellent response to many of Greninja's problems. Mega Gengar haunts Greninja's defensive threats with Shadow Tag, can switch into Fighting-type attacks, and in general can take out fast offensive Pokemon with Destiny Bond. Talonflame also works well, being able to destroy most Fighting-types and Mega Venusaur, and it can also revenge kill Mega Mawile as long as Mega Mawile hasn't used Swords Dance. Other offensive Flying-types such as Mega Salamence also work well against Mega Venusaur and Fighting-type Pokemon. Finally, offensive Fire-types can work well against the troublesome Mega Mawile. Heatran in particular deserves special mention for its ability to handle Talonflame, and it is even able to use Toxic to defeat defensive Porygon2.
One final piece of support worth mentioning is U-turn and Volt Switch. Because Greninja often has trouble switching in, using these moves can let Greninja take the stage. Great Pokemon to consider for this role include Landorus-T, Scizor, Rotom-W, Mega Manectric, and Rotom-H.