Sidequests are events that can be performed but are not central to beating the game.
To activate this sidequest, tell the Zeal Plant Woman to plant the Seed she received. The Sunken Desert will appear on Zenan in 600 A.D.; enter it and defeat the Retinite to succeed. This sidequest can be done earlier than all others; if you can beat the Retinite, you can obtain a lot of high tech items and equipment early in the game.
Simply enter Ozzie's Fort by flying there with the Epoch, and defeat the Mystical Knights. Magus's best equipment can be obtained through this route. It also nets reduced item prices in Medina in 1000 A.D.
Origin of Machines
Take Robo to the Geno Dome, where he will discover that Mother Brain has gone crazy and has started killing humans. Play the three puzzles and defeat Mother Brain; you can get the Ribbon and Robo's best equipment this way.
First you need the Moon Stone; find it in the Sun Palace in 2300 A.D. You'll have to battle Son of Sun to access it. Take it back to the Sun Keep in 65000000 B.C. and place it in there, then go to 1000 A.D. and check up on it. It's missing; head to the Snail Stop and buy some Jerky. Take it back to 600 A.D. and give it to the Porre Elder's Wife. Then head to the Porre Mayor's house in 1000 A.D. and speak to the mayor; he will give up the Sun Stone for free.
Check out the Northern Ruins in 1000 A.D.; Cyrus haunts them. Go to Choras in 600 A.D. and speak to the Carpenter; he will lament that his Tools have been lost. Travel to 1000 A.D. and borrow some from that era's carpenter's wife, and take them back. The Carpenter will repair most of the ruins; kill the existing monsters there, and pay him 2000g to fix up more of the area. Kill the monsters again, and pay him another 2000g. The Northern Ruins will then allow you to reach several Sealed Chests and Cyrus's tombstone; take Frog there with the Masamune, and the sword will upgrade as Frog comes to terms with Cyrus's ghost.
Firstly, head to Choras in 600 A.D. and talk to Toma; he will give you his soda. Take it to 1000 A.D. and the West Cape, and pour it on his grave; he will appear and tell you where the Giant's Claw is. Enter it and find the Rainbow Shell; it will be carried back to Guardia Castle. Then, head to 1000 A.D. and enter the castle; the king is on trial for supposedly stealing the shell. Go through the treasury to get a shell fragment; the party will then confront Yakra XIII in the trial room. Defeat him to complete the sidequest; Melchior will forge the best quality weapons from the Rainbow Shell.
Firstly, complete the game normally by going through the S.S. Zelbess and defeating the Marbule Sage. After completing the Dead Sea, take Fargo to see his counterpart on the S.S. Zelbess in Home World. The ship will be steered to Marbule; exit and defeat each and every Lagoonate and Mantarrey on the island. Soon, Marbule will be restored, granting access to the Master Hammer and other bonuses. Be mindful to complete this as soon as you complete the Dead Sea; many players miss it because the window of opportuntiy is small.