Head south a bit, save and go inside the house. In the living room, shoot the gray blinds located northeast, and proceed into the kitchen. Here, head down then open the blinds for Skill Upgrade C (x2). Go back to the previous room. Go upstairs. Try to enter the bed room to trigger a cut-scene. When you regain control. leave the house and step on the portal.
You'll be at the Yuriev Institute. Just follow the trio around this place -- triggering cut-scenes each time you catch up. The people here do have interesting things to say, so be sure to talk to them. You'll eventually find yourself at a Gas Station. Save, blast the boxes for Revive S (x2) and go north. Blast the crate onboard the truck for a treasure chest with Med Kit M (x2). Back-track then head east 3 screens. You can destroy the cabin at the third screen, to uncover a forbidden device. (It doesn't have any use for now.)
At the 4th screen, follow the path until you reach a fork. Take the lower path, and blow up the rock for a treasure chest with Skill Upgrade B (x4). Go back, proceed down across the log. Take the lower path north, knock the log down to create a makeshift bridge. Cross it to the other side, and move along the path to the next area.
Here, continue right, then northwest. Knock the log down to get across the river. Save and open the treasure chest near the save point for Antidote H (x2). Back-track and head north to the next area. Continue along the path until you see 2 logs. Go north across the thicker one to the other side. Blast the tree to your right, then go east along the hidden path. Go down the ledge for a treasure chest containing a Boost Max. Go down again and, make your way back to higher ground by heading east. Once there, cross the log and continue north to the next area.
After that short cut-scene, defeat the infected U.R.T.V.s. These things do pack a punch, but are weak against thunder. So be sure to have Shion in for this fight. Their weak zone is CC. Save your game, then head west to the next area. There will be some more cut-scenes, and a boss fight.
This is an easy fight. But it can also frustrate you to no end, if you don't know what to do. First your party should consist of: KOS-MOS, Jr., & MOMO. Stock all your characters to full, then attack a few times to charge your boost gauge. I also recommend casting both Aura Sword and Attacker ether spells on your party, to put a quick end to this fight.
Now be sure to boost your characters in this order: Jr. (execute 2 triangle attacks) -> KOSMOS (attack with square-square-O-O-O) -> Jr. (use O-O-O).
That should do it. Since Jr should deal as much as 1000-1300 HP worth of damage per shot (if you cast both Aura Sword & Attacker on him), while Level 4 is suspended in mid-air. If the boss survives that however, just wait for it to fall back down then pelt 3 O attacks at it using MOMO.