| ステージNo. | タイトル | 概要 |
| 通常ステージ | ||
| 0 | COMMON DESCENT | オープニングステージ |
| 1-1 | ADAPTIVE RADIATION | |
| 1-2 | GENETIC DIVERSITY | |
| 1-3 | SUBSPECIES | |
| 1-4 | SILENT MUTATION | |
| 1-5 | FOUNDER EFFECT | |
| 1-6 | APOPTOSIS | 1面ボス |
| 2-1 | FRAMESHIFT MUTATION | |
| 2-2 | RADIOISOTOPE | |
| 2-3 | PREADAPTATION | |
| 2-4 | HOMOLOGOUS RECOMBINATION | |
| 2-5 | INTROGRESSION | |
| 2-6 | NECROSIS | |
| 3-1 | GENE DUPLICATION | |
| 3-2 | HORIZONTAL GENE TRANSFER | |
| 3-3 | SELF-ORGANIZATION | 巨大なUFOと戦うステージ。 |
| 3-4 | NONSENSE MUTATION | |
| 3-5 | STRUGGLE FOR EXISTENCE | |
| 3-6 | DESCENT WITH MODIFICATION | |
| 0 | BACK MUTATION | エンディングステージ |
| エクストラステージ | ||
| X-01 | NEUTRAL MUTATION | |
| X-02 | DISCONTINUOUS REPLICATION | |
| X-03 | ANTIMORPH | |
| X-04 | AMORPH | |
| X-05 | LEADING STRAND | |
| X-06 | BASE EXCISION REPAIR | |
| X-07 | MISSENSE MUTATION | 2-1を逆にしたようなステージ。 |
| X-08 | TUMOR | 多量のノーマルインベーダー編隊をどんどん倒すステージ。 |
| X-09 | REPLICATION FORK | |
| X-10 | POINT MUTATION | |
| X-11 | NEOMORPH | |
| X-12 | ALLELE | |
| X-13 | PROOF-READING REPAIR | |
| X-14 | MISMATCH REPAIR | |
| X-15 | GENE CLUSTER | |
| X-16 | HYBOMORPH | |
| X-17 | ORC | |
| X-18 | GENETIC DRIFT | 高速でシャッターを抜けていく、障害物コース |
| X-19 | NONSTOP MEDIATED DECAY | ボスラッシュ |
| X-20 | ORDER FOR FREE | "THANK YOU FOR PLAYING." Ver.2の最終ステージ |
| X-21 | GAIN OF FUNCTION | |
| X-22 | TELEOMORPH | |
| X-23 | POINT DELETION | |
| X-24 | INTERSTITIAL DELETION | |
| X-25 | TERMINAL DELETION | 対THE SUN VER.2 |
| X-26 | NUCLEOTIDE DELETION | 対 GIGANTIC-UFO VER.2 |
| X-27 | GENE DELETION | 前哨戦のSPIDERの絡む高速シャッター細道のほうが難関 |
| X-28 | CHROMOSOMAL DELETION | 対 UNKNOWN VER.2 |
| X-29 | PROGRAMMED CELL DEATH | ボスラッシュ(VER.2ボス版) |
| X-30 | LOCUS | "EVOLUTION NEVER ENDS." Ver.3の最終ステージ |
| キメラステージ | ||
| C-1 "SILVER HAWK" 「ダライアス」 | ||
| C-1A | CAPTAIN NEO | 「ダライアス」1面に似た地形のステージ。ボスはKING FOSSIL |
| C-1B | I CAN NOT APE | |
| C-2 "INTER GRAY" 「ナイトストライカー」 | ||
| C-2A | URBAN TRAIL | |
| C-2B | BURN ALT AIR | |
| C-3 "BLACK FLY" 「メタルブラック」 | ||
| C-3A | BORN TO BE FREE | |
| C-3B | BEFORE TEN ORB | |
