The story follows Sonic, Sally, Tails, and Knuckles as they follow Dr. Eggman through different areas as he hatches various plans in succession, with the core goal of retrying his mind control cannon from Sonic Colors. Team Sonic usually runs into these situations unintentionally, finding Animals or Wisps in trouble, Orbot or Cubot carrying out orders, or robots walking around where they should not be. Along the way, the team have several side-adventures where they help Animals, Wisps and Chao with issues or just travel new places. Another subplot involves Team Sonic going on the hunt for Master Emerald fragments after Knuckles was forced to shatter the Master Emerald to stop Eggman from stealing it.
The last story arc revolves around Dr. Eggman who has stolen the Chaos Emeralds and drained them of their power to provide the last fuel needed for his mind control cannon. Team Sonic thus set out to reclaim the drained Emeralds before facing Eggman in a final showdown. Amidst this, Sonic reabsorbs the Chaos Emeralds' energy back into the Emeralds as Eggman uses his mind control cannon on him and becomes Super Sonic. Using his newfound power, Sonic destroys the mind control cannon and peace reigns over the world once more, though Eggman still gave the heroes the slip.
Sonic Runners is a 2D side-scrolling runner with stages that can be played in a minute or two. The player can tap to perform jumps and move the characters. Using Chao, Buddies, items and radio controlled toys, the player's objective is to get the highest score for a level. By doing so, the player can also collect Crystals, which increase the score as long as the player is keeping the combo going.
At the end of a majority of chapters (Unless the plot doesn't involve him like "Ring Hill", or they simply don't run into him, which usually hails an item of some kind instead.), the player also has to engage in boss battles with Dr. Eggman, who has variations on his Egg Mobile. These variations have differing weapons, but commonly involve dodging weapons centered around Spiked balls and jumping into the Yellow Ball contained in others, which will fly back into his machine and damage him.
Progressing the game's episode as Sonic will eventually unlock more playable Sonic series characters, such as Princess Sally Acorn, Miles "Tails" Prower (unlocked by clearing Chapter 10 and entering Chapter 11) and Knuckles the Echidna (unlocked by clearing Chapter 16 and entering Chapter 17:"Goodbye Greenery"). Additionally, the game will be updated to include more characters as well. Each character has their own different action and their levels can be raised using Rings collected in the stages.
The characters are best used in "Specialist Areas". While the levels are playable as any character, specific character types are more suited to exploring these levels, with more accessible areas using their abilities. The regions themselves carry specific aesthetics (Windy Hill = Speed, Sky Road = Flight, Lava Mountain = Power, etc.). An emblem next to the chapter title on the menu screen notes which type is recommended.