1 Meter: HP double > light Ankle Slicer > HP double > light Ankle Slicer > HP double > light Ankle Slicer > Shadow Call of the Earth ender (61%)
2 Meter: HP double > light Ankle Slicer > HP double > light Ankle Slicer > HP double > Shadow Ankle Slicer > Shadow Call of the Earth ender (68%)
( Damage calculation notesThese damage numbers were achieved after heavy Ankle Slicer opener, followed by a counter breaker. Keeping the initial combo as small as possible helps isolate the counter breaker damage, but this is an unlikely scenario in real matches. You can expect your damage to be much higher if you counter break in the middle of a normal combo.)
Notes: Thunder's damage is very high after a counter breaker, especially the no-meter version which is the second highest in the game only to Mira. During regular play, if you counter break in the middle of a combo instead of after just one move, you can expect this damage to be well into the high 70%s if you use both stocks of shadow meter. Thunder's light Ankle Slicer linker is the only choice, since Triplax and higher strengths of Ankle Slicer are much slower. There is a version of the 1-meter combo that uses shadow Ankle Slicer instead of the shadow ender for the same damage, but shadow Call of the Earth lets you juggle for more damage and also causes a hard knockdown for setups, so it is vastly preferred in this very specific combo. However, if you see a non-counter breaker lockout in the course of regular play, know that throwing shadow Ankle Slicer in your combo to quickly increase the ender level is a great use of meter.
Both these moves are largely safe on block. Triplax moves Thunder forward and is a great move to catch people trying to jump away from command grabs, because it hits quickly. Be careful, though, because Triplax can be easily shadow countered; it always hits at least twice, and shadow counters are fast enough to interrupt any hits past the second hit. If you can train yourself to press shadow counter as soon as you see Thunder turning around at the start of Triplax, you will have success stopping this move. Shadow Triplax has one hit of armor, even when used as a shadow counter, so you can blow through some predictable pokes and start a grounded combo.
Ankle Slicer is a low attack that crushes lows and swings Thunder backwards before he lunges forwards, avoiding some attacks. It's useful to catch people trying to backdash or otherwise walk out of range of Thunder's pressure. Lastly, back throw counts as an opener; as Thunder's combo trait, it is directly cancelable into doubles and linkers.
To start a combo on the ground, Thunder sticks with his standard openers. However, if he lands shadow Call of the Earth, or a Sammamish and then uses the Skyfall followup, he will be able to do a brief juggle combo. Typically, Thunder players will use a flipout attack here for a quick reset, or they will attack with some normals and special moves to build up some extra white life so the next opening leads to a bigger cashout.
Ankle Slicer is a fast, damaging linker but the higher strengths are easier to break, since Thunder winds up for multiple swings. Shadow Ankle Slicer completes its five hits very fast, which can make lockouts hurt for two bars. Triplax is one of the few linkers that hits 2, 3, and 4 times for light, medium, and heavy, so be on the lookout for that. Back throw is also a linker (again, Thunder's combo trait), which means you can do two back throws in a row (as an opener, then a linker), and all manuals are possible after back throw. Back throw can be teched while in a combo using LP+LK, but the timing is as tight as breaking a light manual and the throw comes out with linker timing (which is much earlier than a light manual would occur), making it difficult to defend against.
Ankle Slicer will build Thunder the meter he needs to be threatening with shadow Call of the Earth, so it's the recommended ender to use early in the fight. Otherwise, Thunder's damage enders are good choices to use. see the two Call of the Earth enders being used. Regular Call of the Earth is strong damage but can be quick rised so the fight returns to neutral, while shadow Call of the Earth either acts as a hard knockdown if you don't followup with a juggle, or gives a reset opportunity in addition to strong shadow damage. Triplax ender has situational uses, but Thunder's floaty jump hinders some of the traditional wall splat mixups, so Thunder will have to use backdash or other tricks to bait throws here. Sammamish as an ender is both a launcher and a hard knockdown, so you can choose to charge a Call of Sky buff and still have time to apply ambiguous offense here.

This move works well in conjunction with Thunder's excellent dragon punch, Sammamish. All versions of Sammamish are projectile invincible, which gives Thunder an option against some zoners, and they are also upper body invincible, useful for anti-air and certain approaches. Thunder has three different followups to any Sammamish, whether it hits, whiffs, or is blocked. Use Surprise Knee (LK) if you want to cause a flipout and do a fast mixup, or use Skyfall (HK) if you want to stomp on top of somebody's head. You can delay Skyfall and make it a crossup in some situations, and also mess up punish attempts on the shadow version. Dropkick (MK) will keep Thunder's horizontal momentum if pressed early enough, which gives him a way to fly across the screen quickly and attack some zoners. Be careful, though, as all followups are very unsafe on block. Shadow Sammamish is completely invincible, making it Thunder's primary reversal option; without meter, Thunder must either backdash or block on his wakeup, as none of the regular Sammamish versions can avoid attacks that hit Thunder's waist or below.
Thunder also has Call of Sky (PPP), a special move that calls a bolt of lightning down to strike Thunder and power him with lightning, giving him access to a single-use invincible instinct dash. Call of Sky is slow, but Thunder gains access to the dash nearly instantly (on frame 13) and keeps it even if he gets hit, so it can be useful as an approach through powerful zoning moves or to power up your mixup game after a knockdown. The Call of Sky lightning bolt can also destroy projectiles for a brief period of time when it strikes Thunder, but the window is short. The one-time-use instinct dash automatically expires after 10 seconds if not used.
Thunder's Ankle Slicer battery ender is particularly important, since having meter available makes Thunder a much more pronounced threat; if you have bar already, use his other enders such as Sammamish or Triplax to apply mixups, such as jumping HP cross-ups, tick grabs, empty jump lows, and empty jump grabs. Or, you can use Call of the Earth ender to earn big damage and go back to neutral. For reversals, Thunder can really only use shadow Sammamish, but when your opponent is anticipating this reversal, bring out the shadow Call of the Earth to make him really frustrated and scared to approach a knocked down Thunder. If you're getting zoned out, use Sammamish to avoid projectiles; if the zoner is particularly troublesome, use the Dropkick followup to fly across the screen and try to knock him down, but this is risky if it misses or is blocked. You can also inch your way forward with forward dash, or use Call of Sky situationally to get you closer. If you're really struggling, activating instinct should get you the rest of the way there.