Outside

Upon arriving at the Cipher Lab, you will encounter the Hexagon Brothers: Cipher Peon Resix (L14 Slugma, L17+ Houndour (S)), Cipher Peon Blusix (L11 Horsea, L12 Goldeen, L17+ Spheal (S)), Cipher Peon Yellosix (L12 Electrike, L11 Chinchou, L17+ Mareep (S)), Cipher Peon Browsix (L14 Hoothoot, L17+ Baltoy (S)), Cipher Peon Purpsix (L10 Koffing, L11 Grimer, L10 Tentacool, L7+ Gulpin (S)), and Cipher Peon Greesix (L9 Oddish, L9 Cacnea, L9 Shroomish, L8 Lotad, L9 Pineco, L17+ Seedot (S)). You must defeat one of them before entering the building. It is recommended to fight those you are not weak against first.

Consider replacing Teddiursa, Ledyba, and Poochyena with Houndour, Mareep, and Spheal for a more balanced party. Teddiursa's Pickup ability is useful for obtaining items after battles.

Purify and train Shadow Pokémon at Mt. Battle. You should be strong enough to clear Areas 1-2. Completing Area 2 for the first time rewards you with TM05, which is advised to teach to Vaporeon or Spheal.

On 1F, you will face Cipher Peon Corla (L14 Duskull, L14 Skitty). A Healing Machine is available here. Take the elevator down.

On B1, the path splits. Go right to face Cipher Peon Javion (L13 Doduo, L14 Taillow). Use the elevator at the end and head south to battle Mesak.

On B3, head left and then north to encounter Cipher Peon Nexir (L14 Swinub, L13 Shuppet, L14+ Spinarak (S)). Collect the Revive and take the staircase up.

On B2, head south to eavesdrop on Prof. Krane and Cipher Admin Lovrina. Continue south to be confronted by Cipher Peon Solax (L15 Ralts, L16 Voltorb, L16 Bagon, L14+ Numel (S)). Board the elevator.

On B3, an elevator beside the one you exited from leads to a Healing Machine. Opening a chest triggers a battle with Cipher Peon Digor (L17 Abra, L16 Machop, L16 Feebas, L16 Makuhita). Go back down and head west to face Cipher Peon Crink (L14 Snorunt, L14 Barboach). Go north to find Cipher R&D Morbit (L16 Spoink, L14 Lotad, L14 Staryu).

The path splits north and south. Take the north path to find Cipher Peon Cabol (L15+ Carvanha (S), L15 Magnemite, L15 Psyduck, L16 Remoraid). Go south for another split. Head right to meet Cipher Peon Meda (L16 Natu, L14 Nincada, L15 Wailmer). Head right and then east to face Cipher R&D Elrok (L17 Swablu, L16 Wynaut, L15 Corsola) and Cipher R&D Coffy (L14 Dustox, L17 Wingull, L15 Qwilfish, L16 Pineco). Board the elevator.

On B1, walk towards the hall's end to encounter Cipher R&D Klots (L16 Snubbull, L16 Kecleon, L15+ Shroomish (S)) and Cipher Peon Nopia (L15 Jigglypuff, L17 Chimecho, L16 Dunsparce). Shroomish is worth catching. To defeat Klots's Kecleon, use different type attacks due to its Color Change ability. Klots drops an ID Card. Use it to open the elevator to the next floor.

On B3, walk up the staircase to meet Cipher Peon Naps (L18 Murkrow, L18 Rhyhorn, L18 Slakoth, L18 Beldum). After Prof. Krane joins your party, grab the Leaf Stone and head to 1F.

Use the Healing Machine on B1 to heal your Pokémon before the boss battle.

As you approach the exit on 1F, you will be confronted by Cipher Admin Lovrina.