Strong style (Introduced in Black Label and Version 1.5) gives the player max firepower as well as bombs but makes the game slightly harder.

Hypers are built up through large combos, attacking enemies at close range, and collecting green bee medals.

This is integral to scoring, as point items would have their value multiplied by how many hits are on the combo gauge, and with enemies firing large streams of bullets at the player, the player can maximize combo scores by learning when to activate their hypers and where to activate them so the enemies don't get destroyed too quickly.

Arrange A (or Ver L) uses the same hyper system as Dodonpachi Daioujou, with only one ship to pilot (the narrow shot ship from Daioujou, piloted by the element doll Leinyan) Black Label and Black Label novice add a new red gauge for scoring, much harder patterns, and a new final boss encountered at the end of the game if you fulfill certain conditions, Zatsuza.

Arrange B on the PC release is a mode where you can play through singular stages with any ship you like, with altered bullet patterns for enemies and bosses.

Smartphone mode, exclusive to the iOS and Android versions, includes a new Slaughter-Menace meter that would influence a point multiplier, a revamped hyper system where it increases power by spinning the ship with the touchscreen, and a new soundtrack.

A Zatsuza practice mode exclusive to the Nintendo Switch release will allow players to challenge the boss with 3 lives and maximum bomb stock.

After the turmoil caused by the assault on Lunapolis which sparked the "Blissful Death Wars" (as depicted in the previous installment), peace seems to have been restored, with the legendary DonPachi Corps retreating to its HQ in a space-time fold.

Six years later, anomalies are detected in the space-time fabric, yet tests reveal nothing out of order, with the portals regularly functioning for both teleportation and time travel; also, the leader of the DonPachi squadron Colonel Godwin Longhener (a descendant of the deranged Schwarlitz Longhener who once commanded the Donpachi Corps like he had) dismisses the matter due to the lack of actual danger.

Nevertheless, a technician delves deeper into the anomaly, discovering that something has infiltrated the HQ computer systems and is using the portals to send large quantities of materials and data to the past, spreading out like a virus and quickly evolving.

In an ironic twist, the virus is discovered to be the program originally installed in the Element Dolls six years ago, now reaching beyond the DonPachi Corps programming and seeking to annihilate the human race in retaliation for their "enslavement" (after the war, they met a rather cruel demise at the hand of their own human creators) by waging war in the past rather than in the present: unsettled, the Colonel authorizes the last transport ship to time jump in order to fight back the invasion before future changes.

And once again, the three pilots jump back in time to 2008 and enter the fray, the transport ship being targeted as soon as it exits the portal: the Element Daughters, gigantic evolutions of the Dolls, are awaiting...

After beating the game, the entirety of the plot is revealed: one of the Dolls, EXY, interfaced with the enemy computer network at the end of DaiOuJou, managing to shut it down but succumbing to madness soon thereafter.

Overwhelmed by the sea of new information, she turned against her human pilot, killing him and herself and becoming the parasitic virtual entity detected by DonPachi HQ; still following her original programming, she created the Element Daughters and the robotic army featured in the game in a desperate attempt to destroy the installation that would start the chain of events leading to the Blissful Death Wars - presumably, DonPachi Corps HQ itself at the time of the elite squadron's birth.

As the pilot jumps back to the future, he comes to finally realize how, instead of preventing the bloody future depicted in the series, Next EXY actually triggered it: he/she is forced to watch, powerless, as Longhener is appointed as the commanding officer of the DonPachi Corps with the rank of General, the Daughters standing beside him - the date being just a few years before the start of the Blissful Death Wars.

In Arrange A, Leinyan appears in front of EXY in her ending of Dodonpachi Daioujou, and manages to console her into giving up her plan, preventing the chain of events that would lead to this game.