Ninjask is the standard lead of one of the most powerful team archetypes of all time: the Baton Pass chain. It can be extremely hard to stop there, which makes Ninjask and the team around it a huge threat worth keeping in mind. Ninjask also works well outside of Baton Pass teams; it can pass boosts to dangerous sweepers such as Metagross and Marowak, which might very well start sweeping your team on turn four if you don't watch out.
The goal of this set is to stall for turns and avoid damage with Substitute while allowing Speed Boost to increase Ninjask's Speed, in order to gain boosts that can be Baton Passed. If Ninjask can keep up a Substitute, it should then use the turn to set up Swords Dance. However, Hidden Power Flying is an option as Ninjask's Substitutes won't stand up to any attacks at all, and after Ninjask has revealed Silver Wind, opponents that expect a mono-attacking Ninjask might be tempted to send in Heracross.
In the earlier days of FRLG, a variant with Baton Pass, Protect, Substitute, and Swords Dance was common; however, the general consensus is that Ninjask should be able to do damage if it gets the chance. Do not underestimate Ninjask's own attacking and sweeping capabilities.
A Jolly nature lets Ninjask combat opposing Ninjask. If Ninjask's HP divisible by 4, it will only need to use Substitute thrice to activate the Berry boost, but the ability to put up four Substitutes can be handy as well; however, Ninjask will have to watch out for Tyranitar.
You would be surprised at how many people expect Ninjask to only be able to set up and Baton Pass, and not to be able to deal any actual damage; unpredictability is a definite advantage in the 386 metagame. Ninjask can easily switch in on Choice Band users locked into Earthquake or Hidden Power Bug, set up a Swords Dance on the switch, and then attack. Hidden Power Rock is primarily to surprise Zapdos and Salamence, but also OHKOes most Fire-types.
An Adamant nature gives this sweeper-oriented Ninjask a handy power boost; it is fast enough even without the boost from a Jolly nature. However, a Jolly nature can be useful for other Ninjask.
With sky-high Speed and decent Attack, Ninjask can put the hurt on opponents when equipped with a Choice Band. If Ninjask is paired with Magneton, it can use Baton Pass first to check for Skarmory; much the same goes for Dugtrio to pick off the likes of Metagross. In the same vein as the Aerodactyl + Dugtrio strategy, this Ninjask is an excellent kamikaze attacker to break Substitutes from Pokemon such as Raikou and Celebi, which lets Dugtrio finish them off afterwards. Hidden Power Rock takes down Flying-types such as Aerodactyl, while Shadow Ball does the same for Gengar and Aerial Ace for Heracross. Hidden Power Flying can be used over Aerial Ace, but Ninjask will have to forgo Hidden Power Rock as well.
Adamant is the recommended nature as Ninjask is fast enough without the Speed boost from Jolly, and it appreciates the power boost an Adamant nature provides.
Substitute + Protect combo lets Ninjask stall for many more turns unless its opponent packs a multi-hit move such as Rock Blast.
Checks and Counters
Skarmory completely shuts down all Ninjask. Suicune, although it takes more damage from Ninjask, can counter Baton Pass variants with Roar. Weezing resists Ninjask's STAB Bug moves and can erase its stat boosts with Haze, but Ninjask will still be able to pass Substitutes.
Also, be on the watch for Quick Attack, ExtremeSpeed, and of course Fake Out. Choice Band Medicham's Fake Out will deal over 70% damage to 252/0 Ninjask. However, it can only switch in on a predicted Protect, as Ninjask will almost always have a Substitute up. Arcanine is a potent counter to Ninjask as it not only resists Ninjask's Bug-type STAB moves, but also has Intimidate to lower Ninjask's Attack, a Fire move to beat down its Substitutes, and priority ExtremeSpeed to take it out for good.