Shaymin-S can successfully employ the SubSeed strategy due to its extremely high Speed. In fact, it is outsped only by Jumpluff in the sun and Ludicolo in the rain, whereas Prankster Whimsicott has priority SubSeed. Fortunately, all three of these are relatively uncommon in Ubers, so the competition is virtually nil. While it may be tempting to use Whimsicott, remember that Shaymin-S has a great base 120 Special Attack, allowing it to take on a more offensive approach. As with all SubSeed strategies, one starts by switching in Shaymin-S to scare off certain whales or behemoths. Then, it can Substitute on the switch and begin to wreak havoc, alternating between Substitute and an attack after Leech Seed. Alternatively, Seed Flare can force switches, as the Special Defense drops cause plenty of fleeing for Shaymin-S to take advantage of. Air Slash fills the last slot to annoy any victim that stays in; its health will be slowly sapped by Air Slash, unable to fight back due to the excessive flinching. Hidden Power Fire and Earth Power are also options to hit Scizor and Dialga, respectively, but Air Slash's high flinch chance makes it too good to pass up.

The EVs accentuate Shaymin-S's strong points, Special Attack and Speed. There is little use in investing in defenses, as by Uber standards, 100 / 75 / 75 is rather poor. A Timid nature takes advantage of Shaymin-S's unique Speed tier, ensuring it is not outsped by any Arceus or Darkrai; a Special Attack-boosting nature is less important because the offensive moves are used only for their secondary effects, not for damage output. Hidden Power Ice can surprise Dragon-types such as Rayquaza and Garchomp, but as mentioned, Shaymin-S will find it difficult to fit it onto its moveset.

Tons of Pokemon aid Shaymin-S in endlessly annoying its opponents with SubSeed. Wobbuffet is especially notable, as it can prey on the Choice Scarf users that aim to take down speedy Shaymin-S. In addition, the blue blob can use Encore to give Shaymin-S a free opportunity to set up. Deoxys-S is another great partner, as it provides entry hazard support to whittle down the opponents' health from the number of switches the SubSeed strategy forces. Forretress also pairs well in this regard, providing Rapid Spin support and setting up Toxic Spikes to further wear down walls.

Shaymin-S without Hidden Power Fire must be wary of Scizor, as its priority Bullet Punch bypasses Shaymin-S's high Speed. Skarmory also walls Shaymin-S lacking Hidden Power Fire, using Roost to heal off damage and phazing Shaymin-S out. Groudon provides necessary support to take these threats out. Rayquaza sets up on any set lacking Hidden Power Ice, outspeeding and destroying Shaymin-S after boosts from Dragon Dance. Likewise, Dialga will take advantage of any Shaymin-S set without Earth Power. Without a Special Defense drop provided by Seed Flare, both Calm Mind Giratina and Calm Mind Giratina-O have the potential to outstall Shaymin-S.

When equipped with a Choice Scarf, Shaymin-S becomes a great revenge killer, outspeeding the entire unboosted tier. It can also function as a lead, flinching threats such as Darkrai to death before they can even respond. Seed Flare is the main STAB attack, having the ability to neutralize switch-ins with a Special Defense drop. Air Slash complements this move very well, also receives STAB, and can KO opponents lacking a resistance simply through repeated flinches. Earth Power provides coverage against those that resist Seed Flare and Air Slash, namely Steel-types such as Dialga, Jirachi, and Metagross. Hidden Power Ice has the most utility on a Choice Scarf set, revenge killing other common Pokemon with a +1 boost such as Garchomp, opposing Shaymin-S, and Dragon Dance Salamence and Rayquaza.

Leaf Storm is a more powerful alternative than Seed Flare right off the bat, and it is viable on a set that switches as often as this. However, it drops Shaymin-S's Special Attack by 2 stages, making additional hits very weak; repeated Seed Flares will most likely increase damage output due to the Special Defense drops it can inflict, too. Another way to augment power is with the nature. Modest is preferred for a revenge killing role, as Choice Scarf Shaymin-S outspeeds even Timid Choice Scarf Palkia. However, a Timid nature is viable if one prefers Shaymin-S to be a lead, as the extra Speed is needed to outpace Darkrai. Either way, it is a great check to standard Rock Polish Groudon, as even at +2, Groudon is outsped and OHKOed by Shaymin-S.

Hidden Power Fire is an option over Hidden Power Ice to incinerate Scizor, but this choice leaves Shaymin-S vulnerable to other Shaymin-S sets. Rapid Spin support is appreciated, as Choice Scarf Shaymin-S will most likely be switching constantly. Likewise, entry hazards support is appreciated to wear down opponents. Shaymin-S must watch out for Pokemon that resist Grass-type moves or have high Special Defense, such as Rayquaza, Dialga, and Latias, as they can come in and set up with ease. Mixed Dialga is thus a good teammate since it is able to deal with Blissey, Latias, Skarmory, and Swords Dance Rayquaza for Shaymin-S.

With excellent Special Attack and Speed stats even by Ubers standards, as well as a movepool that gives it good coverage, Shaymin-S makes a dangerous special sweeper. Seed Flare is what makes Shaymin-S so fearsome, as with Serene Grace there is a high chance of inflicting that Special Defense drop. After that, Shaymin-S can plow through the opponent or continue to assault the switch-in with its powerful attacks. One must be wary of spamming this move, however, as the prevalence of Pressure users means its PP could drop at an alarming rate. Air Slash is a secondary STAB move that has a great flinch chance, decimating switch-ins before they can even retaliate in conjunction with the Special Defense drops which Seed Flare can cause. Earth Power provides coverage on Steel-types such as Dialga, who resist both Seed Flare and Air Slash. However, this is hardly a problem if they have been inflicted with the Special Defense drops. The final slot is given to Hidden Power Fire, which KOes Scizor and Skarmory, both of whom 4x resist Seed Flare.

A few other moves can work in the last slot as well. Hidden Power Ice is one option, KOing Lugia if it has already been hit with a Special Defense drop. This also applies to Latias, Giratina, and Giratina-O, who could otherwise take Hidden Power Ice with ease. On the other hand, Growth forgoes coverage and gives Shaymin-S the ability to boost its Special Attack instead of relying upon Seed Flare's Special Defense drops. While the Attack boost would be unhelpful for the most part, +1 in Special Attack will allow Shaymin-S to take down Pokemon it would otherwise fail to KO. This becomes more useful in the sun, as Growth will grant a +2 boost to Special Attack; Shaymin-S can then proceed to decimate weakened teams with its decent three-move coverage of Seed Flare, Air Slash, and Earth Power.

The EVs are straightforward here, bolstering Special Attack and Speed to their maximum levels. Once again, a Timid nature is preferred over a Special Attack-boosting nature because of Shaymin-S's unique base Speed. The final 4 EVs are placed in Special Defense to ensure the maximal number of switch-ins to Stealth Rock. The IVs serve a very particular purpose, namely to reduce Life Orb recoil, allowing Shaymin-S to survive 11 whiplashes instead of 10. Speaking of items, Life Orb is preferred to maximize damage output, which is especially devastating in conjunction with Seed Flare's effect. However, Leftovers provides passive recovery to increase Shaymin-S's survivability, especially when used with Growth, as Shaymin-S will then be powering up itself and the extra power of Life Orb is secondary.

The easiest way to take down Shaymin-S is with faster attackers. Priority easily KOes this frail flier, especially after Stealth Rock damage and Life Orb recoil, as it has no priority of its own to retaliate with. Furthermore, Scizor can Pursuit a fleeing Shaymin-S, ensuring that it will die to Stealth Rock the next time it switches in. Choice Scarf users are in the same boat, especially those that resist Seed Flare and Air Slash, such as Jirachi, Metagross, Heatran, and Dialga. Once again, Wobbuffet deals with these Choice-locked opponents, and can help Shaymin set up Growth with Encore. Ho-Oh walls Shaymin-S cold, as it can easily take Air Slash with its massive Special Defense. Groudon is a helpful partner, KOing most Steel-types with Earthquake and checking Ho-Oh to an extent.

A Choice Specs set is a different take on Shaymin-S, affording it immediate power without the recoil of Life Orb. Seed Flare maims any switch-in that does not resist Grass-type moves, and even those that do pack a resistance must be wary of the Special Defense drops; if Shaymin-S outspeeds, the opponent will inevitably fall. Air Slash provides a second STAB move, and is especially great because of its 60% chance to flinch the opponent. Due to the fact that Choice Specs powers up Shaymin-S's special attacks, less Air Slash uses would be needed than without the boost, and thus there is a higher chance the opponent will be flinched to death before it can retaliate. Earth Power provides additional coverage, hitting the Steel-types that resist Grass- and Flying-type moves, such as Dialga and Jirachi. Hidden Power Ice rounds out the coverage, OHKOing Dragon-types such as Rayquaza and Garchomp; tread carefully around Choice Scarf variants of the latter, though, as they will outspeed and deal massive damage if not OHKOed.

Hidden Power Fire is an alternative in the last slot, as with it Shaymin-S will be able to beat Skarmory and Scizor. The EVs are distributed to maximize power and Speed, indicative of an offensive set; the last 4 EVs are placed in Special Defense to avoid an even HP stat, providing more switch-ins into Stealth Rock. The choice between a Modest and Timid nature depends on whether one wants the extra power afforded by the former or the extra Speed to get the jump on Darkrai and maximum Speed Arceus formes afforded by the latter. For example, Modest Choice Specs Seed Flare has a 58% chance to KO Blissey, provided the first Seed Flare inflicts the Special Defense drop. Such a feat is not possible with a Timid nature.

Pokemon that can take a Seed Flare are generally the best counters to Shaymin-S. Blissey can stall it out with a combination of Wish and Protect, cripple it with Thunder Wave or Toxic, or deal massive damage with Ice Beam. Skarmory can either Whirlwind Shaymin-S or KO it with Brave Bird. Any Pokemon with a powerful STAB move can easily revenge kill Shaymin-S, such as Palkia and Kyogre. Wobbuffet is a good partner to deal with these threats. Ho-Oh is not afraid of any move Shaymin-S carries, and it can use its Fire- or Flying-type STAB to take out Shaymin-S. Ferrothorn and Bronzong can survive long enough against Seed Flare to 2HKO Shaymin-S with Gyro Ball.