Lugia is undoubtedly one of the sturdiest physical walls in the game, but is actually numerically stronger special defensively even with the standard spread. This results in a very evenly rounded wall that can take almost any attack; it's extremely difficult to OHKO something with a 106/130/154 defensive layout. Lugia's good 110 base Speed is also higher than that of many Ubers, including Rayquaza, Ho-Oh, Palkia, Groudon, and Kyogre without Choice Scarf.
Lugia has been and still is one of the most reliable walls in the Uber metagame. While Giratina gives it competition, it does sport several advantages, which it should utilize as much as possible. First and most importantly, it receives an immediate recovery move in Roost and therefore isn't forced to use the less efficient Rest and Sleep Talk. It also doesn't have a weakness to Dragon-type attacks, allowing it to pseudo-haze Latias, Latios, and occasionally Rayquaza, without too many problems. Additionally, it is much faster and can use Ice Beam, which is generally a very effective move in Ubers.
Lugia is, above all else, a counter for physical Pokémon such as Groudon and Metagross; both Roost and Reflect aid its mission, with Roost as the critical recovery move and Reflect slicing physical damage in half. Whirlwind is another move geared towards stopping physical attackers. While Lugia is sturdy enough to take 72%-85% from even a Choice Band Groudon's Stone Edge, it can't keep up with a Choice Band Metagross's Meteor Mash or Life Orb Rayquaza's Outrage that is boosted multiple times. Therefore, it needs to remove the boosts by forcing the offending Pokémon to switch out. If used after one's own Forretress has set down Spikes or Stealth Rock, Whirlwind also works to inflict some residual damage upon the opponent.
As is often the case, the fourth slot involves a more complicated decision. For Lugia, viable options there include Toxic, Light Screen, and Ice Beam. Toxic is Lugia's best opportunity for any significant damage to Pokémon not weak to Ice-type moves, such as Darkrai and Mewtwo, and is usually the best of the three options; it is also excellent to ravage some of Lugia's targets, such as Rayquaza and Groudon. However, Toxic is utterly ineffective against Metagross and leaves Lugia with no offensive moves, leaving it a facile target for Taunt from Darkrai, Mewtwo, and others; also, all of Lugia's exertions may be rendered useless by a timely Blissey Aromatherapy. Considering Toxic's foibles and the fact that Toxic Spikes is quite popular on Uber teams, one may choose the next option, Light Screen. Although Lugia is predominantly a physical wall, it does have excellent base 154 Special Defense, and Light Screen capitalizes on that by essentially neutralizing its common weaknesses of Electric-, Ice-, Ghost-, and Dark-type attacks, and protecting it from Water- and Dragon-type attacks. Light Screen has the same issue as Toxic in that it leaves Lugia vulnerable to Taunt, though, and makes Lugia thoroughly incapable of inflicting any damage without field effects in place. Ice Beam is a proactive solution that will not deter Metagross, but hits super effectively on Groudon and Rayquaza. Unfortunately, the damage it inflicts is lackluster on anything else, and only has a 2.6% chance of OHKOing the standard Rayquaza even after one round of Life Orb damage.
Lugia may sometimes drop Whirlwind so that it may use both Ice Beam and Toxic. This allows it to deal quick damage to both Groudon and Rayquaza, while being able to inflict status on Mewtwo and Darkrai that think they can switch in believing that Lugia has Ice Beam and not Toxic. Toxic can act as a semi-phazing move as the opponent will not want to stay in to face the increasing poison damage, and unlike Whirlwind it can permanently cripple a Pokémon. However, without Whirlwind, Lugia does not have a quick answer to stat boosters and Baton Passers such as Ninjask.Team Options & Additional Comments >>>
Lugia's talents can extend to special sweeping after boosting with Calm Mind. While Latias may appear to run the bulky Calm Mind course more effectively due to a better special movepool, lack of an Electric-type weakness, and far superior Special Attack, Lugia can boast that it isn't locked in and annihilated by Metagross Pursuit and doesn't care about Normal Arceus with ExtremeSpeed. The general idea of this set is to Calm Mind against Pokémon such as Groudon that wouldn't be capable of hurting it and attack with Ice Beam. Whirlwind blows away anything that tries to match Lugia, especially Calm Mind Kyogre. However, Thunder is a viable option over Whirlwind to hit Kyogre directly; it also serves to hit Metagross more effectively. The EV spread given for this set lets Lugia Calm Mind ahead of a Palkia Thunder without fear. Also, it can outspeed any non-Choice Scarf Garchomp, allowing it to faint the beast with an Ice Beam before it can do too much damage to Lugia. Lugia also keeps a lot of its physical durability, for example, a Choice Band Groudon Stone Edge only does 85.58% at maximum, so Lugia will be able to stall out its effectively 4 PP (after Pressure slices its original 8) assuming there aren't too many critical hits or the random numbers remain medium or low. However, make sure you have spun away Stealth Rock.Team Options & Additional Comments >>>
This particular Lugia is designed to cripple, or at least hamper, many of its common switch-ins while still serving the role of a defensive counter. However, beware that "normal" Lugia sets will almost always use Leftovers, making the lack of Leftovers recovery give away that fact that you are holding Choice Specs.
Trick is the main feature of this set and allows Lugia to disable more defensive switch-ins such as Blissey and Latias. For example, if the standard Latias (Timid, 112 HP / 204 SpA / 0 SpD) is Tricked on the switch-in and loses its Soul Dew in exchange for Lugia's Choice Specs, Lugia will beat it 1 on 1 with Ice Beam (assuming that Latias does not get multiple critical hits or that you are without Roost). If Latias chooses to lock itself into Recover or Roost, Lugia can easily PP stall it out. Trick will also allow Lugia to disable Pokémon like Calm Mind Mewtwo as they switch in. By investing a small amount in Special Attack when aided with Choice Specs Lugia can cripple its more offensive switch-ins such as Kyogre. Although Aeroblast appears to be an oddball in this set, it provides general coverage, and is surprisingly powerful when powered up by Choice Specs. If you are having problems predicting between Ice Beam or Thunder while Choice Specs is still held by Lugia, you can't go wrong with Aeroblast.Team Options & Additional Comments >>>
This set takes a radically different approach from the other Lugia sets, focusing on Lugia's offensive capabilities instead of its defensive prowess. While Lugia's low base 90 Special Attack may seem unappealing, its bulk, Speed, and powerful Aeroblast more than make up for this setback.
Aeroblast is the crux of this set, being more powerful than a Life Orb-boosted Ice Beam from Mewtwo. With Stealth Rock, +1 Aeroblast 2HKOes Wobbuffet and nearly OHKOes Mewtwo, Lugia's most common counters. It can also 2HKO common threats, such as Giratina-O, Latios, Groudon, Scizor, and Forretress, as well as OHKOing Darkrai and Rayquaza after SR. In addition, it has a chance to 2HKO max HP Kyogre after Stealth Rock, though Calm Mind variants with Rest / Sleep Talk can cause trouble.
Roost is a vital move for this set, as it allows Lugia to set up multiple Calm Minds against specially offensive foes, such as Palkia and Dialga. You should choose the last move depending on what your team can handle. Earth Power in general hits Pokemon who resist Aeroblast, such as Steel- or Electric-type Pokemon. Earth Power specifically helps deal with Dialga and Heatran, both of whom may attempt to wall Lugia. Thunder easily defeats Kyogre, opposing Lugia, and Skarmory. It also hits Ho-Oh, though be careful, as sun reduces Thunder's accuracy to 50% and allows Ho-Oh to OHKO Lugia with Sacred Fire. Hidden Power Fighting is a viable option, as it allows Lugia to 2HKO specially defensive Tyranitar after a boost, and OHKO minimum HP Tyranitar after Stealth Rock. While you will no longer 2HKO specially defensive Dialga (thus meaning that Lugia will lose to Bulk Up Dialga), Lugia will still be able to 2HKO max HP Dialga with a boosted Hidden Power Fighting. However, Hidden Power Fighting Lugia will have issues getting past Jirachi and Metagross. Finally, if Steel-types are not a problem, Ice Beam is a possibility to get a quick OHKO on Rayquaza and Garchomp while still 2HKOing opposing Lugia after you gain a boost. Ice Beam will also deal a massive amount of damage to Giratina-O.Team Options & Additional Comments >>>
Rest + Sleep Talk is a potential replacement for Roost, because Roost leaves Lugia open to Toxic; overall, though, it is far less efficient, and with Rest and Sleep Talk, Lugia loses to Groudon. Safeguard and Substitute protect Lugia from status altogether and could be nice on the special attacking set. Aeroblast is a very powerful STAB attack, but won't hurt that much from Lugia's inferior (by Uber standards) 90 base Special Attack, and has very low PP, which is wasted further by Pressure from various Ubers. A gimmicky Choice Band set could work, with the main attacks being Punishment and Avalanche, but Lugia's superior defensive stats indicate that walling threats is generally more common, and at the very least, you should stick to special attacks, which can be boosted by Calm Mind. Thunder Wave deserves mention on Lugia's sets, as it works well with Lugia's high base 110 Speed, so it can cripple many offensive threats, almost destroying any chance of a sweep. However, it is not always the best option, as some of the more common threats for Lugia to handle include Garchomp and Groudon, both of whom are immune to Thunder Wave.
Earth Power can also find a place on the Trick set to better handle Dialga, Tyranitar, and Metagross. However, you are often better off just crippling Tyranitar and Metagross by burdening them with a Choice Specs via Trick. Aeroblast can work as a filler option in the final slot of the Trick set as well. However, because of the low PP and the fact it doesn't hit any of the Uber metagame for super effective damage means you'll often be disappointed. Weather Ball allows Lugia to OHKO Forretress in sunlight, and deal a decent amount to it in rain.
Since Lugia falls prey to Wobbuffet quite easily, it is viable to use Shed Shell with it. Wobbuffet can abuse Lugia's slightly lower Special Attack by using Encore on a weaker attack, or Encoring a set up/status move to start a potentially devastating sweep. It can also use Tickle to lower Lugia's Defense, making it bait for Pursuit-users like Tyranitar and Scizor. Thus, a way to escape Wobbuffet's grasp should be considered when possible. The drawback of course is that Lugia loses its passive Leftovers recovery, which not only slows its recovery, but also tips your opponent off that Lugia is using something abnormal.
Checks and Counters
Lugia can't do anything against Pokémon with Taunt, as its attacks aren't very powerful without any boosts. Calm Mind Mewtwo rips Lugia to shreds, while Mew can set up and Baton Pass away. Darkrai can even put Lugia to sleep and smash it with Nasty Plot boosted STAB super effective Dark Pulses. Toxic is also very debilitating against Lugia without Rest, so a stalling Dialga will beat it.
Calm Mind Kyogre beats Calm Mind Lugia when Lugia is without Thunder through attrition; a six-stage boosted Ice Beam will only do 32% at maximum to a Kyogre, even without HP or Special Defense EV investment.
Tyranitar is one of the very few Pokémon who can conquer Lugia completely, by using sheer force. A Choice Band boosted maximum Attack Stone Edge has an 86% chance of OHKOing the standard Lugia, with Sandstorm in effect, while Pursuit chases down fleeing Lugia, reducing its health to the extent that any reasonable attack will kill it. However, using Stone Edge may be risky, as Roost negates the Rock-type weakness and Pressure eats away at Stone Edge's low PP. Even if it has a Reflect up, Lugia can't take repeated Crunches, because Tyranitar will eventually inflict enough Defense drops to knock Lugia out. However, if those Defense drops do not come in quickly enough, Tyranitar may succumb to repeated Toxic damage.