Reunion with Fiora
Following the events at the end of the previous Chapter you'll be controlling Shulk alone on the Fallen Arm of Mechonis. You'll unlock the Wreckage Beach Landmark and you'll spot the Story Flag just up ahead so go there to trigger another scene. Fiora needs water if she's to recover and from your location, the Silver Wreckage, head south to reach Zakt Spring where you'll find some Clean Water and complete this short Story Quest and trigger more scenes.
We Made It
You'll have a new objective once you regain control and Fiora will join the party with a whole new set of Arts, Skills and Equipment. Being that she's now in a new body, her playstyle has changed dramatically and she's an incredibly powerful party member. You'll want to focus on Agility with her like most characters but she does have some useful Ether Arts which allow her to pair up well with the other Ether based party members such as Melia, Sharla and Riki.
For now, be sure to register the nearby Heart-to-Heart and then head to the east to unlock Jifum Beach along with an Ether Deposit. Head south from here to find a pathway leading up and into a structure that will unlock the Transformer Area. Continue to follow the path to unlock the Ulna Passage Landmark followed by triggering a scene. You'll be forced into a solo battle against three Mechon that should be far below your current Level. Despite being on his own, Shulk should have no issues dealing with this battle, make use of Monado Eater or Buster to end the battle quicker if need be.
After the scenes that follow, you'll be in control of Reyn and Sharla as they search for Shulk and Fiora. Be sure to check your equipment if you've neglected using any of these characters for a while and you'll notice you've unlocked Power Pipe Ruins. Once you're ready, head east to find an Ether Deposit then climb the nearby wall and head north across the field to trigger a cutscene and another forced battle where you should assign Shulk as party leader. You'll be up against two Lv 52 Offensive Mechon and both should be no problem if you're around Lv 57+ so long as you focus on one at a time.
You'll have all four party members available to you following the scene and it's not a bad idea to remove Sharla from the party, Fiora is too useful a character to bench. Take the path to the south to unlock 5th Pulse Zone and then head down to the bottom to find an Ether Deposit and a Lv 57 Unique Monster, Affluent Beleth that you should dispatch. Make your way back up to the top following the battle and exit via the west to unlock the Radiocarpea Landmark before heading down to the west and triggering another scene.
You'll now be in control of the final three party members, Melia, Dunban and Riki. When you regain control, you'll unlock the Inlet Beach Landmark and see a nearby Heart-to-Heart that you should register. Take the pipe now and follow it to find the entrance to the large central structure here on Fallen Arm. Head inside to unlock Hidden Machina Village and trigger a cutscene where you'll complete the Story Quest.
Hidden Machina Village
You'll unlock Hidden Machina Village location upon regaining control and you'll also notice that Fast Travel is available to you once again, even to Bionis. Your task is to speak to the Machina who greeted you a moment ago but pay a visit to the nearby shop to purchase more Arts Manuals and buy some equipment for Fiora. Due to her body, you'll want to purchase equipment for her and based on what type you buy, it will impact on her performance. For now, purchase the Speed set for her and buy all of the Drones to give yourself more options.
Head west to unlock the Junks Landmark and then east from there to unlock Ether Light while also registering the nearby Heart-to-Heart. Although you can accept a Quest or two right now, consider proceeding with the story for now, this will allow you to unlock some more Quests shortly where you can knock them all out at once so head over to Junks and speak with Linada to trigger a scene and then head into Junks itself to trigger more and bring this short Chapter to an end.