For every mission you get an "A" or "S" rank on, you will get a special bonus part. The following are the other requirements to get bonus parts at the store.

MRL-MM/001: Reach AC rank "D"
MWGG-HNRL-100: Reach AC rank "C"
KAW-SAMURAI2: Reach AC rank "B"
MAM-MX/MDD: Reach AC rank "A"
MBT-NI/GULL: Reach AC rank "S"
CWI-DD-30: Defeat E-21 at the Arena
RGI-KDA01: Defeat E-15 at the Arena
KWG-NHZL30 : Defeat E-8 at the Arena
CWR-M70: Defeat D-7 at the Arena
CWM-BM60-1 : Defeat C-7 at the Arena
MWG-SRFE/8: Defeat B-4 at the Arena
MCL-SS/RAY: Defeat A-3 at the Arena
MWG-MG/FINGER : Defeat A-1 at the Arena
CWM-HA40-8: Defeat rank 1 in Extra Arena
MWG-HGB/108: Rank "S" in all missions
KGP-ZXV1: Complete all missions
CCL-02-EI: Complete 10 missions from Crest
MCM-MI/008: Complete 13 missions from Mirage
KEEP-ELIX: Complete 7 missions from Kisaragi
Op-Intensify (All Abilities): Obtain 99% completion of the game.