To get Aerodactyal and Omanyte or Kabuto you must first collect two out of three items.
In Mt. Moon, before the exit, there is a guy you have to fight. If you when, you get the choice of two fossils. The one on the left is the Dome Fossil, which gives you Kabuto. The one on the right is the Helix Fossil, which gives you Omanyte.
Go back to Pewter City, and cut the bush near the Museum. Go through the back door and speak to the guy near the sphere. He'll give you Old Amber, which gives you Aerodactyal.
To get these extinct pokemon, you most beat Koga in Fushcia City and get HM05 in Safari's Zone's secret house. HM05 teaches Surf, in which you can ride a water pokemon. Go back to Pallet after getting HM05 and the soul badge. Surf down the water way south of pallet until you reach Cinnibar Island.
Enter the building to the left of the pokemon center. Proceed right until you reach the last door. Enter the door and speak to the man at the top. Give him either the Helix fossil, Dome Fossil or Old Amber. Leave, re-enter and he'll give you the corresponding pokemon.
