This Chrono Trigger walkthrough starts like most things: at the beginning.  If  you need help with a specific boss, go to Boss Info.  If you are stuck in general, click on one of the links below to go to that section and bypass the first.  Otherwise, Scroll down to see the beginnings of Crono's journey.  Thanks!
Part 3- Search for Magus, Finding Epoch
Part 4- Return to Zeal
Part 6- Death Peak
Part 2- Quest for the Masamune (Magus)
Part 5- Your new Liege
Part 8- Black Omen
Part 7- Side Quests
Part 9- Final Battle with Lavos
Guardia Kingdom, 1000 AD- After chosing your Battle Time System and naming the main character (hereafter referred to as his default name, Crono), you see an overview of Guardia Kingdom in the Year 1000 AD.  Crono is woken up by his mother, who comments about the music of Leene's Bell.  She mentions a fair and tells Crono to get up!  Head downstairs, and your mother will mention that your "inventor friend" (hereafter referred to as her default name, Lucca) wanted you to visit her exhibit at the fair.  After this dialogue, talk to Crono's mom again to get an additional 200 G as allowance for the fair.  Head outside.
  This is kind of up to you; you can go straight to the fair, you can build up levels in Guardia Forest, or you can explore Guardia Kingdom and explore the land beyond the bridge to the Southwest.  Here is an example of the freedom allowed to you by Chrono Trigger.  If you go to the Mayor's Manor near Chrono's House, you can get a tonic and 100 G, as well as learning battle tactics and other facts about Chrono Trigger.  As far as raising levels, I like to get Crono to
at least Level 3, but 4 is better; by Level 4, you will definitely have Cyclone, and well on your way to getting Slash.  In the forest, don't forget to get the Power Tab to the right of the where you enter.  There's not much to the Southwest, but you can get some decent equipment if you have the money, but it's not really necessary.  When you are ready, go to Leene Square (north of Crono's house with balloons coming out of it.
Leene Square- Again, you have a choice on whether to buy items or equipment from stands, bet on racers, compete in a game of skill, battle a giant singing robot, buy some candy, or go to a dance festival.  I would recommend getting some silver points (one way is to bet on the winner, but an easier way to get points is by defeating Gato) because you can get 50 G for 10 Silver points if you don't want to save them (though they will come in handy further along in the game.)  You should have enough money to buy a Karate Gi and a Bronze Helmet, or you might have enough to get the Iron Blade.  Go up into the next section when you are ready.
  Crono is walking around Leene's Bell when he and a young girl run into each other.  She checks on you before realizing her pendant is gone.  Talk to her before going to pick up the pendant (the shiny thing to the right of Leene's Bell.)  After that, she will ask you to show her around (agree), and introduce herself as (hereafter referred to as her default name, Marle) Marle.  Again, you have some choices on what to do, but your actions will benefit or haunt you later.  If you want to be a good boy (sorry), don't take the man's food, return the cat to its owner (press "A" once by it, then walk and talk to the little girl on the other side of the area), take Marle to the Dance Festival and dance, as well as not moving when she wants to get some candy (you'll understand when you get there.)  Talk to some people from the first level after Marle joins you and they will say that Lucca's exhibit is ready in the back of the Fair.  Head to the back and wait for Marle to buy some candy.
  Several bystanders watch as Taban, Lucca's father, promotes her Super Dimension Warp that can move people from one telepod to the next.  Talk to Lucca (girl with glasses on the left pod), and she will teleport you while Marle watches.  After magically being transported, talk to Marle and she will insist on doing it.  It takes considerable more effort for Lucca and her father to get the machine going, but Marle's pendant begins reacting to the energy transfer and a Gate is created, taking Marle into an unknown place.  Lucca isn't sure what went wrong, but take Crono to the Left Pod and prepare to rescue her.  The same phenomenon will happen again, and Lucca mentions that she will join you ASAP.
Guardia Kingdom, 600 AD- Crono will recover from the teleportation and discover himself 400 years in the past.  Battle through the monsters at the mountains (don't forget the two treasure chests) and explore the town.  You can buy some items or equipment if you haven't already, but you can't cross Zenan Bridge.  If you head into the Inn, you will meet the explorer Toma, who will mention something about the Cathedral, but stop once he learns that Queen Leene was found.  Head through Guardia Forest and walk into Guardia Castle.
Guardia Castle, 600 AD- When Crono enters the castle, he is mocked by the two soldiers until the Queen tells them that Crono is a friend of hers.  There is an item in the kitchen (to your right before going in the throne room), but it isn't super.  Go inside and talk to the King and the Chancellor.  Go up the stairs on the left behind the King and go to his chamber to get a powerful Bronze Mail.  Travel back down to the throne room, and go up the stairs to the right.  A knight will give you access to Leene's quarters, grab the Ether in the chest, and talk to the Queen.  She will dismiss the attendants and reveal herself as Marle!  Following a brief dialogue, she disappears.  Take Crono back down to the throne room where Lucca will meet you and reveal that Marle is really Princess Nadia, heir to the throne in 1000 AD.  Lucca remembers that someone was supposed to save her but history has been changed.  Equip Lucca and set out for the Cathedral, the building to the west of the castle.  I recommend building up Lucca until she at least gets Flame Toss and is at Level 3/4 before entering the Cathedral. 
 
Cathedral, 600 AD- Crono and Lucca are greeted by four nuns as they enter the Cathedral, but Lucca catches sight of Leene's Coral Pin and the nuns attack.  These 4 Nagaettes only have 60 HP, but have decent defense and your levels should be enough to get you through this battle.  Have Lucca cast Flame Toss and heal the party with potions while Crono attacks with Cyclone.  After this battle, Lucca will again be attacked by Nagaette, but saved by a mysteriously talking frog.  Agree to accompany (hereafter referred to as his default name, Frog) Frog and play the piano in the upper left to uncover a hidden door.
     Proceed through the next area, fighting monsters and gaining EXP and Tech points as you go.  Go up the stairs on the left side to get the Steel Saber from a treasure chest.  Touch the skull near the door with spikes around it.  The spikes will go down and you can enter a room containing two captured soldiers and a Powertab.  If you go up the stairs on the right, the further door contains 3 monsters disgusied as the King, Queen, and a soldier.  Get the two chests there and then go to your right and go into the temple for Magus.  Ignore the monsters chants and go grab the Speed Belt and Defender from the treasure chests near Magus' statue.  Exit the room and go up the middle of the main area to gain access to the next area of the cathedral.
     Right at the entrance to the next area is a valuable save point.
 
Unmask and defeat Yakra
Meet Marle and show her around the Fair
Join Frog and battle through the monsters at the Cathedral
Go to the Cathedral and battle the 4 Nagaettes with Flame Toss and Cyclone
Visit Queen Leene at the Palace
Visit Lucca's Super Dimension Warp and teleport a 2nd time to find Marle
Move Crono to the Millenial Fair at Leene Square
Hosted by www.Geocities.ws

1