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Stage gameplay[]

A Blood Falcon propaganda poster is shot at, then out crashes Bill Rizer and Lucia through the shot poster, riding on hover bikes. The camera angle scrolls down to reveal that this scene was a video recording from the events of Contra: Shattered Soldier. Two soldiers on hover boards slowly drive underneath a long tunnel, when suddenly the TV monitor crashes, with the two commandos "Bill" and Jaguar appearing through it on Velociraptors sporting distinct colored armor. The two dinos speed onto the street with enemies in hot pursuit. The commandos easily annihilate all opposition, including larger threats such as an armored car and a flying aircraft.

The velociraptors reach the end of the road and plummet to a pit below, with the two commandos jumping off and clinging onto a nearby wall. The surviving commandos are then chased by a large gray beast with a silver helmet. The two climb and avoid enemy soldiers until they reach a spot in the wall without obstacles or barriers. The beast breaks off its mask and continues to assault the commandos, who easily triumph over the now fell beast. It plummets and the commandos climb upward into an opening.

An armored gate blocks their progress. The two eliminate the wall's turret defenses while avoiding lethal containers being fired upon. They destroy the wall sensor and enter the next room, where they rinse and repeat with a second Sensor wall. The two enter the next room, in for a surprise:

- ???: "Well, I never!"
- Plant CONTRA: "What?! You think you can equal the great Plant Contra? Just who do you think you are?"
- ???: "Equal? Hardly. A pansy like you isn't even a decent warm-up. Hah!" (opens fire on Plant Contra)
- Plant CONTRA: "Gyaaaaaaa!!" (falls motionless to the ground, laying on back flat)

The two commandos enter the room:

- Bill: "Hmm... . What's going on here?"
- Jaguar: "It appears one of the four elite has been defeated."
- ???: (slowly turns head to face the two commandos) "You! You're Rizer, Bill Rizer?"
- Bill: "Yeah. And you are?"
- Mystery G: "Well now... Let's just say Mystery G."
- Bill: "Mystery G..."
- Mystery G: "So this is the Ultimate Soldier CONTRA. Let's see if you have what it takes to live up to that title."
- Bill: "What?!"
- Mystery G: "Bwahahahaha! Let's see what you got!"

Mystery G battles the two commandos and is defeated by them.

- Mystery G: "Interesting. You're not bad. Even so, will he be able to face him?"
- Plant CONTRA: "Ooooh... ." (sits up, ash on him blows off)
- Mystery G: "Huh?"
- Plant CONTRA: (hits head) "How could I have been so careless?"
- Mystery G: "Hrmph. Still twitching. But I'm tired of dealing with this weed. Rizer, go ahead uprood it."
- Bill: "Huh?"
- Mystery G: (teleports away) "See ya!"
- Jaguar: "Hey! Wait a minute!"

(brief pause)

- Plant CONTRA: "What? Hey! No! Ahh! Hey! Don't ignore me! How dare you! Listen to me! I don't know who you are, and I don't care. But now you've really made me mad! En garde! Serious mode! Plant Flaassshhh!"

In a flash of light, Plant Contra grows into an enormous plant-like creature and battles the two commandos from the center of the room. Plant Contra is ultimately defeated by the two commandos:

- Jaguar: "Incredible. I can't believe he was a plant cyborg."
- Bill: "Yeah. But right now I'm more interested in that...Mystery G. What's his angle?"

Next: Stage 3