Like in the previous two seasons, color-coordinated episodes indicate that they focus on specified characters.

Episode Episode Title Plot
53 Summer Vacation Begins. The Mysterious Blue Hedgehog

(夏休みが始まります。不思議の青いハリネズミ, Natsuyasumi ga Hajimarimasu. Fushigi no Aoi Harinezumi)

54 Team 7R Reunites! A New Quest Begins

(7R団は再会!新たなる旅が始まります, SebunAru-dan wa saikai! Aratanaru Tabi ga Hajimari masu)

55 Welcome to Mobius. The Green Hill Zone

(モビウスへようこそ。グリーンヒルゾーン, Mobiusu e Yōkoso. Gurīn Hiru Zōn)

56
57 Red Alert! Eggman's Secret Weapons

(非常警報!エッグマンの秘密兵器, Hijō Keihō! Egguman no Himitsu Heiki)

58
59
60
61
62
63
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65 A Black Shadow Descends. Shadow the Hedgehog

(黒い影が下降する。シャドウ・ザ・ヘッジホッグ, Kuroi kage ga kakō suru. Shadō za Hejjihoggu)

66 A Silver Lining. Enter Silver the Hedgehog!

(銀の裏地。シルバー・ザ・ヘッジホッグ登場!, Gin no Uraji. Shirubā za Hejjihoggu Tōjō!)

67
68
69
70
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73 Sonic, Shadow and Silver! The Rival Hedgehogs Unite

(ソニック、シャドウ、シルバー!ライバルハリネズミが団結, Sonikku, Shadō to Shirubā! Raibaru Harinezumi ga Danketsu)

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