■2 x MMI-GAU26 17.5mm CIWS, fire-linked, mounted in head
■MA-BAR73/S high-energy beam rifle
■M2000GX High-Energy Long-Range Beam Cannon
Stored on the left wing, the M2000GX high-energy long-range beam cannon serves as the Destiny's primary long-range weapon. When in use, the cannon unfolds and swivels underneath the Destiny's shoulder while a trigger and guard extend to allow the Destiny to take manual aim. This beam cannon is the mobile suit's most powerful long-range weapon, possessing firepower that is capable of destroying most battleships with a single shot.
■MMI-714 "Arondight" Anti-Ship Sword
Stored on a rack behind the right wing, the foldable MMI-714 "Arondight" anti-ship sword is the Destiny's main close-combat weapon. It is an improved version of the MMI-710 "Excalibur" anti-ship sword. It is normally used against large targets such as the Earth Alliance's GFAS-X1 Destroy Gundam. However, as Paul Lyon's preferred weapon in close-quarters combat and arguably the strongest melee weapon in the Destiny's arsenal, it sees extensive use against all types of enemies.
■MMI-X340 "Palma Fiocina" Palm Beam Cannons
A unique feature of the Destiny is its two MMI-X340 "Palma Fiocina" palm beam cannons. These close-range weapons release powerful energy discharges that are capable of destroying the "Slayer Whip" heat rods of a ZGMF-X2000 GOUF Ignited and even the armored head of the massive GFAS-X1 Destroy. Since the "Palma Fiocina" have only been used in close combat throughout the series and in other related appearances, it is unknown whether they are capable of firing over long ranges. During the final battle of Gundam Seed Destiny, Shinn attempted to use the "Palma Fiocina" to parry the beam sabers of Athrun Zala's ZGMF-X19A Infinite Justice Gundam. However, due to a possible overload or simply because of the superior power in the beam sabers' concentrated beams, the Destiny's hands exploded.
■MX2351 "Solidus Fulgor" Beam Shield Generator
Like its brother unit, the ZGMF-X666 Legend, the Destiny is also equipped with two wrist-mounted MX2351 "Solidus Fulgor" beam shield generators. These generators generate powerful beam shields that allow the Destiny to defend itself from even the combined power of a Destroy's three "Super Scylla" multi-phase beam cannons.
■RQM60F "Flash-Edge 2" Beam Boomerang
The Destiny is equipped with two RQM60F "Flash-Edge 2" beam boomerangs. They are upgraded forms of the Sword Impulse's RQM60 "Flash-Edge" beam boomerangs. One is stored on each shoulder, similar to the ZGMF-X09A Justice. Unlike previous models, the Destiny's beam boomerangs also double as beam sabers, though they rarely see use in this form. Shinn uses these versatile weapons in a wide variety of ways, such as using them to distract opponents while he closes in for a close-range attack, or to destroy several enemy units in its trajectory.
■Hyper-Deuterion Nuclear Reactor
The Destiny is powered by a hyper-deuterion nuclear reactor, giving it a self-replenishing power reserve. Despite this amazing power source, the Destiny is quick to run out of available power in a fight, with one of its engagements with the Strike Freedom ending in a retreat due to energy depletion. However this would end up being retconned in the Special Edition where the Destiny returned to the Minverva for repairs.
■Neutron Jammer Canceller
Like the ∞ Justice,Strike Freedom and Legend, the with a Neutron Jammer Canceller to allow it's nuclear reactor to work in areas affected by Neutron Jammers.
The ZGMF-X42S Destiny uses the Gunnery United Nuclear-Dueterion Advanced Maneuver operating system, (MOBILE SUIT NEO OPERATION SYSTEM Ver.1.62 Rev.29).
■Wings of Light
The "Wings of Light" is the Destiny's most unique design feature. Utilizing a variant of the Voiture Lumiere propulsion system in conjunction with Mirage Colloid particles, the Destiny is capable of achieving very high speeds while leaving behind a trail of visible after-images to confuse its enemies. One of Shinn's signature attacks with the Destiny is utilizing the Wings of Light's massive acceleration in conjunction with the "Arondight" anti-ship sword. With the Wings of Light active, Shinn rushes into close combat range with unprecedented speed and impales his target with the Arondight. Most instances of Shinn performing this maneuver have been done against larger, less maneuverable opponents such as the Earth Alliance's Zamza-Zahs, Gelles-Ghes, and Destroys, which lends some doubt as to how effective this attack would actually be against units of similar mobility such as the Strike Freedom and Infinite Justice. As shown during the final battle of Gundam Seed Destiny and in an FMV cutscene in Dynasty Warriors Gundam 2, the speed and after-images granted by the Wings of Light allow the Destiny to effectively dodge the multi-directional attacks of the DRAGOON System. The Wings of Light were actually reverse engineered from the DSSD's Stargazer's Voiture Lumiere propulsion system, unlike the Strike Freedom, who derived the system directly from the Stargazer.