Alternate secret factors happen when you use a ultimate jutsu to finish off characters that have some sort of relationship with the other character.

Music:
1st track: Naruto Shippuden Ultimate Ninja Storm Generations Opening
2nd track: Naruto Shippuden Ultimate Ninja Storm 3 OST - Stage of Dust and Tumult
3rd track: Naruto Shippuden Ultimate Ninja Storm 3 OST - Bond of Snow Tears
4th Track: Naruto Shippuden Ultimate Ninja Storm 3 OST - With the Shinobi World at Stake


Extra Tags - Do not read below the line.
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Naruto Uzumaki (Young) with 1-Tail awakening
Naruto Uzumaki (Teen) with 4-Tail awakening
Naruto Uzumaki (Teen) with Tailed Beast Chakra Mode awakening
Naruto Uzumaki (Sage Mode) with 6-Tails awakening
Sasuke Uchiha (Young) with CS2 awakening
Sasuke Uchiha (Teen) with CS2 awakening
Sasuke Uchiha (Taka) with Mangekyo awakening
Sasuke Uchiha (Five Kage Summit Arc) with Susano'o awakening
Sasuke Uchiha (Eternal Mangekyo Sharingan) with Susano'o awakening
Sakura Haruno (Young)
Sakura Haruno (Teen)
Kakashi Hatake (Teen)
Kakashi Hatake (Adult) with Sharingan awakening
Asuma Sarutobi
Asuma Sarutobi (Reanimated)
Ino Yamanaka (Young)
Ino Yamanaka (Teen)
Ino Yamanaka (Fourth Great Ninja War)
Shikamaru Nara (Young)
Shikamaru Nara (Teen) with Shadow mode awakening
Shikamaru Nara (Fourth Great Ninja War)
Choji Akamichi (Young)
Choji Akamichi (Teen)
Choji Akamichi (Fourth Great Ninja War) with Butterfly mode awakening
Might Guy
Tenten (Young)
Tenten (Teen)
Tenten (Fourth Great Ninja War)
Neji Hyuga (Young) with Byakugan awakening
Neji Hyuga (Teen) with Byakugan awakening
Neji Hyuga (Fourth Great Ninja War)
Rock Lee (Young) with Eight Gates awakening
Rock Lee (Teen) with Eight Gates awakening
Rock Lee (Fourth Great Ninja War)
Hinata Hyuga (Young) with Byakugan awakening
Hinata Hyuga (Teen) with Byakugan awakening
Hinata Hyuga (Fourth Great Ninja War)
Shino Aburame (Young)
Shino Aburame (Teen)
Shino Aburame (Fourth Great Ninja War)
Kiba Inuzuka (Young)
Kiba Inuzuka (Teen)
Kiba Inuzuka (Fourth Great Ninja War)
Jiraiya
Sai
Minato Namikaze (Jonin)
Minato Namikaze (Hokage)
Chiyo
Obito Uchiha
Zabuza Momochi
Zabuza Momochi (Reanimated)
Haku
Haku (Reanimated)
Killer Bee
Killer Bee (Samehada) with Tailed Beast State awakening
Ay (4th Raikage)
Mei (5th Mizukage)
Ohnoki (3rd Tsuchikage)
Hashirama Senju (First Hokage)
Tobirama Senju (Second Hokage)
Hiruzen Sarutobi (Third Hokage)
Tsunade (Fifth Hokage)
Yamato
Danzo Shimura
Kimimaro Kaguya
Gaara (Young)
Gaara (Teen)
Garra (Kazekage)
Garra (Fourth Great Ninja War)
Temari (Young)
Temari (Teen)
Temari (Five Kage Summit)
Temari (Fourth Great Ninja War)
Kankuro (Young)
Kankuro (Teen)
Kankuro (Five Kage Summit)
Kankuro (Fourth Great Ninja War)
Orochimaru
Kabuto Yakushi
Kabuto Yakushi (Snake Cloak)
Kabuto Yakushi (Sage Mode)
Suigetsu
Karin
Jugo
Pain
Konan
Itachi Uchiha (Akatsuki) with Susano'o awakening
Itachi Uchiha (Anbu)
Itachi Uchiha (Reanimated) with Yasaka Magatma Ultimate Jutsu
Kisame Hoshigaki
Deidara
Tobi (Goofy) with "Madara" awakening
Tobi (Fourth Great Ninja War)
Sasori
Hidan
Kakuzu
Masked Man
Torune
Fu
Cee
Darui
Chojuro
Ao
Akatsuchi
Kurotsuchi
Kurenai Yuhi
Anko Mitarshi
Shizune
Tayuya
Jirobo
Kidomaru
Sakon
Madara
Nagato (Reanimated)
Mifune

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