The game has a total of five stages, many of which share design similarities to Super C (the NES version of Super Contra). The three odd-numbered stages (1, 3, and 5) are played from a side-view perspective, while the two even-numbered ones (2 and 4) are top-view. The soundtrack consists primarily of arranged background music from the original Contra, with the exception of a few tunes (namely the Area 2 theme, the Stage Select theme, the sub-boss theme in Area 3, and the ending theme). Operation C was the first Contragame to feature auto-fire as a default feature, resulting in the removal of the Machine Gun power-up from previous games. The Laser Rifle is also removed, leaving only the Spread Shot and Fire Gun from Super C. However, the game introduces a new Homing Gun that fires bullets that chase after enemies. The Spread Shot starts out as a three way shot, but it can be upgraded to a five way version after picking it up a second time. Unlike Super C, the Fire Gun does not have chargeable shots, while the Barrier and Rapid Bullets power-ups are not featured in this installment either.
The player takes the role of Bill Rizer, who must neutralize an enemy force that is secretly storing an alien cell in their base. As with the previous Contra games for the NES, the exact details of the game's settings varies between supplemental materials: in the Japanese version, the enemies are identified as the army of an unnamed hostile nation that is seeking to use an alien cell to produce weapons; in the American versions, the enemies are working for an alien entity calling itself "Black Viper". Likewise, the main character's identity was changed from Bill (the Player 1 character from the previous arcade and console games) to Lance (the Player 2 character from the previous installments as well).