Bubble is in Pencil's Alliance. They seem to have a good relationship in the first three seasons, though Pencil would sometimes mock Bubble's seemingly low intelligence. Bubble usually accompanied Pencil wherever she went, and Pencil revived Bubble numerous times in BFDIA, bringing her back onto the show (though not officially).
Episodes suggesting a friendship
In "Take the Plunge: Part 1", Pencil yells at Ice Cube to stop squeezing Bubble before she pops. During the challenge, Bubble says that they, along with Pencil, should form an alliance. Pencil agrees.
In "Barriers and Pitfalls", Bubble tells Pencil that she was afraid of being popped earlier but is feeling better and doesn't think she will be popped, only to get popped much to Pencil's concern. Bubble waits with Match for Pencil to come back from rescuing Blocky before starting the race.
In "Are You Smarter Than a Snowball?", Pencil says that she likes ice cream cake and Bubble agrees. She later asks Match how she could kill her own friend after she pops Bubble.
In "Sweet Tooth", Pencil and Match are surprised when Bubble manages to count to three and come to the conclusion that she isn't dumb after she reaches eight.
In "Bridge Crossing", when Bubble falls off the cliff due to the bridge breaking, Pencil jumps down to rescue her.
In "Power of Three", Bubble and Pencil are placed on the same team, along with Match.
In "Cycle of Life", Bubble tries to tell Pencil and Match about her vote status but is popped by the Announcer before she can finish. Pencil is angry at the Announcer for this.
In "Don't Lose Your Marbles", Pencil calls Snowball out for killing Bubble. Pencil talks about how cool it is that her entire alliance made it to the final 11. Pencil listens to Bubble vent about how mean Blocky is and calls him a murderer for popping her. Pencil later asks who they're still waiting for to turn in their balls and Bubble answers Eraser and Ice Cube.
In "Half a Loaf Is Better Than None", Pencil calls out to Bubble to save her from falling off the cliff. Bubble and Pencil are saddened by Match's elimination. Ice Cube comes up to them and asks if she can join their alliance, which Pencil agrees to. Bubble thinks Match would be angry if she found out she was replaced, only for Pencil to make an excuse that Ice Cube is only a substitute. During the challenge, the alliance try to work together to jump over a hurdle, however only Bubble was able to make it across.
In "Vomitaco", Pencil suggests that she and Bubble play catch but their game is cut short due to Ice Cube not having arms. Pencil asks Bubble if the giant barf bag is filled with actual vomit and the Announcer tells her it's colored water. When Rocky fills it with actual vomit, Pencil throws a bowling ball at him. Bubble tells her that was mean. Pencil wants to make ice cream with Bubble. However, this resulted in Pencil grabbing Ice Cube, putting her on top of a cone, and then putting vomit and whip cream on her. Bubble tastes the "ice cream" and is so grossed out by the taste that she falls off her platform and pops.
In "Bowling, Now with Explosions!", Pencil doesn't take off any points from Ice Cube and Bubble since they are in her alliance.
In "The Reveal", Pencil tells Bubble not to open Leafy's present because it could be a trap. Bubble tells Pencil that she can do what she wants and opens the gift anyway. In the frisbee contest, Pencil partners up with Bubble and Bubble agrees. They end up placing first in the contest.
In "Reveal Novum", Pencil and Bubble can be seen talking to each other at the beginning of the episode.
In "Rescission", Pencil kills Firey in retaliation for him killing Bubble with a laser. Bubble is saddened when Pencil is eliminated and asks Ice Cube what they should do.
In "Return of the Hang Glider", Pencil tries to vote for Bubble to win Dream Island but switches to Leafy when everyone threatens to slap her.
In "Get Digging", when Ruby asks if Bubble is in the alliance, Pencil says "Sadly she's dead". Later Match and Pencil realize they can easily blow Bubble back to life but are talked out of doing it because of Ruby.
In "Insectophobe's Nightmare 3", Pencil blows Bubble back to life. Pencil explains to Bubble that they shouldn't have to listen to the Book of BFDI Tips and Tricks because it's over a billion years old and was written by Golf Ball. Pencil is upset when Bubble ends up getting popped by a shard of glass.
In "Zeeky Boogy Doog", Pencil and Match recover Bubble twice.
In "The Long-lost Yoyle City", Pencil tries to help Bubble pass off a tree in order to fool the Firey Speaker Box into letting her stay.
In "Welcome Back", when Pencil falls off the ledge, Bubble tries to pull her up, but strains herself and pops, dropping Pencil. Later, Book and Pencil recover Bubble.
Despite Pencil's abusive behavior towards Bubble before her elimination, "Enter the Exit", Pencil still included her in a doodle of her alliance members on her desk.
In "Get in the Van", when Bubble tries to talk Pencil into letting Book and Ice Cube stay at the dance party, Pencil tells her that they can't stay because they're only alternates.
In "It's a Monster", when Pencil tells everyone to hold their breath because they are about to drive through the Goiky Canal, Bubble gets worried and says that the Goiky Canal is over 500 miles wide. Pencil tells her to calm down and just do it.
In "Welcome Back", Bubble gets in front of the camera to eat a gumdrop, which seems to be interrupting Pencil. When Pencil is devastated by their lost work, Bubble tells her that she doesn't feel bad since she's had her life disappear so many times that it no longer affects her.
Episodes suggesting a conflict
In "Are You Smarter Than a Snowball?", Pencil comes to the conclusion that Bubble is too dumb to count three. She and Match then rip up Bubble's test since they think she would fail anyway.
In "Sweet Tooth", Pencil and Match continue to call Bubble dumb. Bubble attempts to prove them wrong by counting to three but dies before getting to three again.
In "Vomitaco", when Pencil says she's glad that she didn't pick the taco contest, Bubble asks why and Pencil pops her saying she doesn't want to answer any stupid questions.
In "Reveal Novum", when Bubble asks if Pencil's eyes hurt after eleven hours of keeping them open. Pencil replies no and then angrily asks Bubble what's gotten into lately.
In "Zeeky Boogy Doog", Pencil scolds Bubble for popping for no reason, Bubble apologizes.
In "Getting Teardrop to Talk", Bubble starts to feel like her alliance is changing when Pencil and Match cheer over Lightning zapping Spongy. Pencil gets mad at Bubble for telling Lightning to do what he thinks is right and demotes her to Bember, much to Bubble's sadness. When Pencil tells Lightning to go zap Fanny, Bubble tries to stop him but Pencil talks Bubble out of stopping Lightning by reminding her of her Bember status. Bubble lets go of Lightning reluctantly and cries as Fanny is electrocuted while Pencil grins at Fanny's suffering alongside Match.
In "Get to the Top in 500 Steps", Bubble mentions that she does not need Pencil, saying "When I struggle, I don't need a stern leader! I don't need Pencil! I needed you." This implies that Bubble does not find Pencil to be very sympathetic, and likely no longer likes her.