The player's team first enters the cave with Team Charm. The exploration team first enters the first Monument Room; from there, if the I, C, and E stones are in the Treasure Bag the team can proceed to the Regice Chamber; if they do not have the required stones, the team enters Ice Aegis Cave, where these stones can be collected. After defeating Regice in the Regice Chamber, the team proceeds to the second Monument Room, where they will proceed either to the Rock Aegis Cave or Regirock Chamber depending on if they have the R, O, C, and K stones. After defeating Regirock in the Regirock Chamber, the team proceeds to the third Monument Room, where they will proceed either to the Steel Aegis Cave or Registeel Chamber depending on if they have the S, T, L stones and two E stones. After defeating Registeel, the team proceeds to the Aegis Cave Pit, where Regigigas is battled along with a group of four Hitmonlee and four Bronzong.
Unown stones are sometimes dropped by Unown when defeated; the stone dropped corresponds to the letter or symbol of the Unown knocked out. All 28 Unown stones have no practical use outside Aegis Cave; all stones other than C, E, I, K, L, O, R, S, and T have no practical use in the dungeon, either. They cause 60 damage if thrown at a Pokémon (90 damage if the Pokémon has the IQ skill Power Pitcher) and can be sold for 10 Poké.
Unlike most other dungeons, the cave's intermissive rooms have no exits. A player attempting to leave through the south will encounter an invisible wall, and will be unable to pass. The only ways to leave the cave are to complete it or use an Escape Orb.