This is the most straightforward and effective set for any Rain Dance team. Thunder, although a risky move to use outside of rain, is necessary because of its sheer power. Prankster makes Thunder Wave a superb support move, as it lets Thundurus paralyze threats such as opposing Swift Swim Pokemon. Rain Dance can also be considered in this moveslot if maintaining rain is very important to your team. Hidden Power Flying hits several common threats—namely Ludicolo, Toxicroak, Abomasnow, and Hitmontop—for a large amount of damage.
Lastly, Substitute and Protect are both viable options, and your pick should depend on your playstyle and team. With Prankster, Thundurus can always set up a Substitute before the foes are able to attack, which can be handy when facing Dragon Gem-boosted Draco Meteors, as Substitute not only wastes their Gem but also causes their Special Attack to drop needlessly. With proper prediction, Thundurus can sometimes even set up a free Substitute, making it more difficult to take down. For example, if Thundurus is paired with a Fake Out user, both foes might use Protect to negate the Fake Out, letting Thundurus set up a Substitute unscathed. However, for those that do not like the 25% HP loss along with the prediction that comes with Substitute, Protect is a safer alternative. It is a rather straightforward move, but unlike Substitute, it cannot be reliably used every turn.
Thundurus's unique typing and ability, along with its superb Speed, sets it apart from Electric-types such as Zapdos, Raikou, Rotom-W, and Jolteon, and makes it a better fit for rain teams. Thundurus is immune to Earthquake, which single-handedly makes it better than most other Electric types. Thundurus also gets access to Prankster, Thunder Wave, and Rain Dance—a combination not found on any other Pokemon.
Thanks to its excellent Special Attack and Speed stats, Thundurus is able to outspeed several threats and damage them severely. A Timid nature and 252 Speed EVs take advantage of Thundurus's stellar Speed, allowing it to outrun common threats such as Garchomp and Terrakion, avoid being flinched by Rock Slide, and take them out with its powerful moves. Alternatively, Thundurus can use a spread of 252 HP / 248 SpA / 8 Spe with a Modest nature; although this reduces Thundurus's Speed, it grants Thundurus excellent bulk and allows it to survive almost any attack.
As this Thundurus is built for use on a dedicated rain team, recommended partners to it include Politoed, Ludicolo, Kingdra, and Toxicroak. Pairing lead Thundurus with a Fake Out user is a very viable strategy against opposing weather teams; this allows for several options depending on your opponent's leads. For example, should they lead with a weather inducer of their own, a simple switch into Politoed not only gives you weather control, but also forces your opponent to switch out. If they don't lead with their weather inducer, Thundurus still has a variety of options, including spamming Thunder Wave and slowly crippling your opponent's team. As a first-turn Fake Out is a nuisance to many players, they often opt to double Protect, allowing Thundurus to use Rain Dance, set up a Substitute, or even switch out.