Time to Fly!
Now that everyone is back together, you need to find a way to get to Summers. Unfortunately you cannot teleport there because you haven't visited yet. The only option seems to be Jeff's crashed machine in Threed. Go outside the building and the Runaway Five will give you a ride to Threed. Head into the prison where Jeff crashed his Sky Runner and it'll be completely repaired. When you climb in, it'll take you to Winters. Here, Dr. Andonuts will remodel the Sky Runner and he mentions a shiny spot nearby. Remember the Your Sanctuary location Jeff passed earlier in the game? Head there now. Make sure to use the Revitalizing Device first to restore everyone's HP and PP for free.
Make sure you call Escargo Express and grab the Bag of Dragonite you found from Monkey Caves and give it to Paula. Enter the cave and head straight to the boss, Shrooom!
After the boss battle, you will have access to the fourth Your Sanctuary location, Rainy Circle. Enter and store the melody with the Sound Stone.
Now would also be a good time to use the pencil eraser on the pencil statue you saw when you came this way as Jeff, but be careful -- There are a lot of really hard enemies beyond the pencil statue, so once you erase it, be sure to hurry back the way you came.
Once back at the lab, use the Revitalizing Device again before talking to Dr. Andonuts and heading for Summers.