Sources: [1] and [2]

• ✔ ABSOL- After beating the game, just climb Realgam tower again and you have another go at catching Absol *INFINITE CHANCES*
• ✔ AIPOM- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Aipom’s trainer will leave, and you can’t get Aipom. *1 CHANCE*
• ✔ ARIADOS- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Ariados’s trainer will leave, and you can’t get Ariados. *1 CHANCE*
• ✔ BAYLEEF - If this guy was your starter but you missed him in Phenac, you can still encounter him in the game room of the Realgam Colosseum. Be careful, he will leave. *1 CHANCE*
• CROCONAW- If you picked Bayleef as your starter, you will encounter him in the Snagem Hideout *1 CHANCE*
• ✔ DELIBIRD- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Delibird’s trainer will leave, and you can’t get Delibird. *1 CHANCE*
• ✔ DUNSPARCE
• ✔ ENTEI- You will fight Dakim (who will have Entei) in two places. First you will fight him in one of the Realgam Colosseum domes, and later you fight him in Deep Colosseum. *TWO CHANCES*
• ✔ FLAAFFY
• ✔ FORRETRESS- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Forretress’s trainer will leave, and you can’t get Forretress. *1 CHANCE*
• ✔ FURRET
• ✔ GLIGAR- Found in Snagem Hideout *INFINITE CHANCES*
• ✔ GRANBULL- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Granbull’s trainer will leave, and you can’t get Granbull. *1 CHANCE*
• ✔ HERACROSS- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Heracross’s trainer will leave, and you can’t get Heracross. *1 CHANCE*
• ✔ HITMONTOP- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Hitmontop’s trainer will leave, and you can’t get hitmontop. *1 CHANCE*
• ✔ HOUNDOOM- After beating the game, just climb Realgam tower again and you have another go at catching Houndoom *INFINITE CHANCES*
• ✔ LEDIAN- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Ledian’s trainer will leave, and you can’t get Ledian. *1 CHANCE*
• ✔ MAKUHITA - Find him in the Snagem Hideout upon beating the game. Not the Shadow Lab, the Snagem Hideout. *INFINITE CHANCES*
• ✔ MANTINE- After you beat the game, you will encounter this pokemon in the room where you originally fought Miror B. *INFINITE CHANES*
• ✔ MEDITITE
• METAGROSS- After beating the game, just climb Realgam tower again and you have another go at catching Metagross *INFINITE CHANCES*
• ✔ MILTANK- After beating the game, just climb Realgam tower again and you have another go at catching Miltank *INFINITE CHANCES*
• ✔ MISDREAVUS
• ✔ MURKROW- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Murkrow’s trainer will leave, and you can’t get Murkrow. *1 CHANCE*
• ✔ NOCTOWL
• ✔ PILOSWINE- Found in Snagem Hideout *INFINITE CHANCES*
• ✔ QUAGSIRE
• QUILAVA- If you picked Bayleef as your starter, you will encounter him in the Shadow Pokemon Lab *1 CHANCE*
• ✔ QWILFISH
• RAIKOU- You will fight Ein (who will have Raikou) In two places. First you will fight him in one of the Realgam Colosseum domes, and later you fight him in Deep Colosseum *TWO CHANCES*
• ✔ REMORAID- After you beat the game, you will encounter this pokemon in the room where you originally fought Miror B. *INFINITE CHANCES*
• SHUCKLE- After beating Gonzap, you will be able to go to the Deep Colosseum. Enter and clear the challenge four times, and then enter again. You will fight Shuckle’s trainer in the final match *INFINITE CHANCES*
• ✔ SKARMORY- Found in the Snagem Hideout after beating the Ranger in the Shadow Lab, which happens after beating the game. Yeah. *1 CHANCE*
• ✔ SKIPLOOM
• ✔ SLUGMA
• SMEARGLE- Found in the Snagem Hideout before fighting Gonzap again. *INFINITE CHANCES*
• SNEASEL- Found in Snagem Hideout *INFINITE CHANCES*
• ✔ STANTLER- Found in Snagem Hideout *INFINITE CHANCES*
• ✔ SUDOWOODO- You will fight Miror B (who will have sudowoodo), in two places. First you fight him in one of the Realgam Colosseum domes, and later you fight him in Deep Colosseum *TWO CHANCES*
• ✔ SUICUNE- You will fight Venus (who will have Suicune) In two places. First you will fight her in one of the Realgam Colosseum domes, and later you fight her in Deep Colosseum *TWO CHANCES*
• SUNFLORA- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Sunflora’s trainer will leave, and you can’t get Sunflora. *1 CHANCE*
• ✔ SWABLU
• TOGETIC- Togetic is the only pokemon in the entire game that you only have one shot at. After you beat the Deep Colosseum, you will eventually be led to the Outskirt Stand where you will fight Togetic’s Trainer. *ONE CHANCE*
• TROPIUS- After beating the game, just climb Realgam tower again and you have another go at catching Tropius *INFINITE CHANCES*
• ✔ TYRANITAR- After beating the game, just climb Realgam tower again and you have another go at catching Tyranitar *INFINITE CHANCES*
• URSARING- Found in the Snagem Hideout before fighting Gonzap again *INFINITE CHANCES*
• ✔ VIBRAVA- Found in either the Shadow Lab or Snagem Hideout upon game completion when the Cipher Peon drops down in that area. If this peon doesn’t drop down, leave the area and keep coming back until he does.. Once you beat the Ranger in charge of that area, Vibrava’s trainer will leave, and you can’t get Vibrava. *1 CHANCE*
• YAMNA

After you capture and purify all of the shadow pokemon, you will be able to get Ho-Oh.