What Game Comes After Naruto: Ultimate Ninja 3? Shippuden: Ultimate Ninja 4

Naruto Shippūden: Ultimate Ninja 4 (Japan, 2007, PS2).

Naming Confusion

• Japan: UN3 → UN4 (Shippūden) → UN5 → UN Impact (PSP) → Storm series
• North America/EU: UN3 → Naruto Shippūden: Ultimate Ninja 4 (2009, PS2) — same game as JP UN4
• Then: Ultimate Ninja 5 (JP UN5, 2009 PS2) → Naruto Shippūden: Ultimate Ninja Storm (PS3, 2008) — 3D arena fighter, new engine

Timeline

1. Ultimate Ninja (2003)
2. Ultimate Ninja 2 (2004)
3. Ultimate Ninja 3 (2005)
4. Shippūden: Ultimate Ninja 4 (2007 JP / 2009 West)
5. Shippūden: Ultimate Ninja 5 (2009 JP / 2011 West)
6. Shippūden: Ultimate Ninja Storm (2008 PS3) — series pivot

So the direct sequel is Shippūden: Ultimate Ninja 4 (PS2).