Ruby started to interact with Pencil as an alliance. In Zeeky Boogy Doog, Pencil noticed Ruby making mistakes. They're friends but sometimes however Pencil mostly blames at Ruby making mistakes. As an alliance, they sometimes work together; Pencil had not yet excluded her from the alliance.
Episodes suggesting a friendship
In Insectophobe's Nightmare 3, Pencil and Ruby both seem pretty happy when Bubble is recovered. Also, they both excuse theirselves during the contest along with Match.
Episodes suggesting a conflict
In Get Digging, Ruby argued to Pencil that dipping wands, and blowing a bubble is so much work; Pencil disagreed. Ruby mentioned to Pencil that Bubble can't "count to 3", But really Bubble was able to count to 3. Pencil told her it's a worth a try. Ruby told her she had better work to do. Pencil told her that she's being weird. She told her she's trying to say their friend.
In Zeeky Boogy Doog, because Ruby recovered Flower, Pencil was about to decide to exclude her from the alliance. But mentioned that she's kidding. Ruby wasn't concerned about Pencil being incinerated by Tennis Ball.
In Get in the Van, Pencil yelled at FreeSmart to get in the van; Ruby was one of them. When Ruby asked who at the peanuts, Pencil told her it was her who ate the peanuts. But Ruby denies. Pencil told her she'd been eating the peanuts.
In No More Snow!, every time Ruby makes a mistake pressing the wrong button, Pencil keeps yelling at her. Until pressing the right button, the red button, Pencil died by getting fried and shrinking.
In Welcome Back, Ruby was blamed by Pencil realized she forgot to remove the lens cap from the camera. When Pencil asked her where did she get the results. Ruby just hid the results and played tricks on Pencil to get it from the edge of the tower, calling her "Pence-Pence"; until Pencil unintentionally went on the other side of the tower. Bubble tried to pull her up but she popped, as a result she fell very high. After being saved, Pencil blamed it on Ruby that it was all her fault. After realizing Ruby getting shattered, Pencil was shocked but then just ignored the accident.