Obtaining these gems will reveal the event of the past. There are Iris gems which not listed page, because you won’t miss them through the story of this game.
Phase 1: After meeting with the drake on Marlind, you will run away to the Sanctuary. Now you should see 2 star marks on your map, Go to the star mark near the save point first (South of the inn and equipment shop). You will meet with Agatha, follow her to the cemetery to trigger another event. After an event, you will get “Library Key“.
Phase 2: Before going to war, speak to Neif who stand near the house where you shot the drake down (marlind). He will tell you about the Iris gems on the sanctuary, so go to the sanctuary to obtain the Green Iris Gem: Eins (on the altar).
You need to speak with Seraph in Lastonbell (visit THIS PAGE for more info about it), go to Cambria Caverns and then head to the northeastern area to get the orb.
Defeat Mutant Hellion: Stheno. Visit THIS PAGE for the guide.
Defeat Mutant Hellion: Goblin Lord. Visit THIS PAGE for the guide. See the map on the screenshot above to know the location :).
Defeat Mutant Hellion Titan, visit THIS PAGE for more info about the mutant hellion.
(I do this quest after meeting with Mayvin on Lohgrin, you may be able to do it sooner).
Go to Pendrago – Knight’s tower. You should see Sergei and townspeople there. Talk to Sergei and then talk to the man on the north (near the gate) to learn about the murderer.
Go to the inn and rest. At night, go to Pendrago Church, see the event and you will get the iris gem.
You can begin this quest, after meeting with Alisha on Griflet Bridge (the bridge has been fixed). Speak to Rose and choose the topic about visiting Alisha on her manor.
Speak to the man with purple star near the great tree. He will tell you about the shiny pretty stone on the Bors ruins. Go to Bors Ruins and open your map, you should see purple star on your map, go there and get the Red Iris Gem: Fyra.
You will find this on Pendrago Shrinechurch. Same location where you find fire tablet.
After the rain in Pendrago has stopped, talk to Eugille (Sparrow Feather member; not sure about his name) on Pendrago. He will tell you about the Iris gems on Gaferis Ruins. So go there and head to the room where you fight Serket.
You will get this while completing the side quest Lord of the Land: Gododdin.
Defeat Dryad to get this gem, visit THIS PAGE for more info about it.
Go to Ladylake Noble District (I do this after beating Asura). See your map, and head to the purple star location. You will see a little kid (goblin hellion) who have stole many things. Now you only need to keep following the purple star on your map, until the event ends ( I choose not to tell them to the guards). You can claim Iris gem:Ek on the Sanctuary now.