| 0 | - | cover | 1 | pencils: Gary Frank; inks: Gary Frank; colors: Brad Anderson | Superman; Brainiac |
| 1 | Title Pages and Publication Information | credits, title page | 3 | pencils: Gary Frank; inks: Jon Sibal | |
| 2 | Chapter One First Contact | cover reprint (on interior page) | 1 | pencils: Gary Frank; inks: Gary Frank; colors: Brad Anderson | Superman; Brainiac; Lois Lane; Jimmy Olsen; Perry White; Catherine Grant; Jonathan Kent; Martha Kent |
| 3 | Brainiac Part 1 First Contact | comic story | 22 | script: Geoff Johns; pencils: Gary Frank; inks: Jon Sibal; colors: Brad Anderson; letters: Rob Leigh | Superman; General Zod (flashback, cameo); Ursa (flashback, cameo); Brainiac; Lois Lane; Perry White; Steve Lombard; Ron Troupe (cameo); Jimmy Olsen; Catherine Grant; Jonathan Kent (cameo); Martha Kent (cameo) |
| 4 | Chapter Two Hide and Seek | cover reprint (on interior page) | 1 | pencils: Gary Frank; inks: Gary Frank; colors: Brad Anderson | Superman; Brainiac Probes |
| 5 | Brainiac Part 2 Hide and Seek | comic story | 22 | script: Geoff Johns; pencils: Gary Frank; inks: Jon Sibal; colors: Brad Anderson; letters: Rob Leigh | Superman; Brainiac; Brainiac Probe; Supergirl [Kara Zor-El]; Brainiac [Milton Fine] (flashback, cameo); Jonathan Kent; Martha Kent (cameo); Lois Lane; Steve Lombard; Ron Troupe (cameo); Jimmy Olsen (cameo); General Zod (flashback, cameo); Ursa (flashback, cameo); Non (flashback, cameo) |
| 6 | Chapter Three Greetings | cover reprint (on interior page) | 1 | pencils: Gary Frank; inks: Gary Frank; colors: Brad Anderson | Superman; Brainiac |
| 7 | Brainiac Part 3 Greetings | comic story | 22 | script: Geoff Johns; pencils: Gary Frank; inks: Jon Sibal; colors: Brad Anderson; letters: Rob Leigh | Superman; Brainiac; Supergirl [Kara Zor-El]; Catherine Grant; Lois Lane; Ultra the Multi-Alien (cameo); Koko; Jonathan Kent; Martha Kent; Steve Lombard (cameo); Ron Troupe (cameo) |
| 8 | Chapter Four Mind Over Matter | cover reprint (on interior page) | 1 | pencils: Gary Frank; inks: Gary Frank; colors: Brad Anderson | Superman; Jonathan Kent; Martha Kent; Lois Lane; Headship |
| 9 | Brainiac Part 4 Mind Over Matter | comic story | 22 | script: Geoff Johns; pencils: Gary Frank; inks: Jon Sibal; colors: Brad Anderson; letters: Rob Leigh | Superman; Brainiac; Supergirl [Kara Zor-El]; Lois Lane; Catherine Grant; Jimmy Olsen (cameo); Steve Lombard; Ron Troupe; Brainiac Probe; Zor-El; Alura; Jonathan Kent (cameo); Martha Kent (cameo) |
| 10 | Chapter Five Triumph and Tragedy | cover reprint (on interior page) | 1 | pencils: Gary Frank; inks: Gary Frank | Superman; Lois Lane |
| 11 | - | comic story | 22 | script: Geoff Johns; pencils: Gary Frank; inks: Jon Sibal, BIT; colors: Brad Anderson; letters: Rob Leigh | Superman; Brainiac; Supergirl [Kara Zor-El]; Lois Lane; Jonathan Kent (dies); Martha Kent; Perry White (cameo); Jimmy Olsen (cameo); Steve Lombard (cameo); Catherine Grant (cameo); Ron Troupe (cameo) |
| 12 | Epilogue | comic story | 9 | script: Geoff Johns; pencils: Gary Frank; inks: Jon Sibal; colors: Hi-Fi; letters: Steve Wands | Superman; Martha Kent; Lois Lane; Jimmy Olsen; Perry White (cameo); Lana Lang (cameo); Pete Ross (cameo); John Henry Irons (cameo), Natasha Irons (cameo); Batman [as Bruce Wayne] (cameo); Alfred Pennyworth (cameo); Brainiac; Jonathan Kent (flashback) |