Mega Man Battle Network 5 received a generally tepid reception from critics, with many finding it too similar to previous entries, and criticizing the aging presentation; in mid-2005, both versions were combined and re-released for the Nintendo DS as Mega Man Battle Network 5: Double Team DS[d], which has updated sound and additional content not found in the GBA versions.

The GBA versions were re-released as part of the Wii U Virtual Console in 2015, and are included in the Mega Man Battle Network Legacy Collection for PlayStation 4, Nintendo Switch and PC (via Steam), released in 2023.

While at SciLab, mysterious agents invade, subduing everyone with sleeping gas, kidnapping Yuichiro, and stealing the friends' PETs and NetNavis.

The agents turn out to work for Dr. Regal and his crime syndicate Nebula, which has returned after being defeated in Mega Man Battle Network 4.

Upon obtaining the report and completing SoulNet, Regal intends to unleash Nebula Grey, a program of pure hatred and darkness, upon it, corrupting all humans and NetNavis in the world.

While the heroes evacuate, Yuichiro stays behind to speak to Regal about their fathers' research while a mysterious voice causes the SoulServer to overload.

[16] Viewers of the anime film Rockman.EXE the Movie: Program of Light and Darkness would also receive a special copy of Team Colonel with an e-Reader card for the transformation "BassCross MegaMan".

The Game Boy Advance versions were re-released onto the Wii U Virtual Console in Japan on September 9, 2015,[17] and in North America on December 12, 2015.

[18] The games are also included in the Mega Man Battle Network Legacy Collection for PlayStation 4, Nintendo Switch and PC via Steam, released in 2023.

[19][20] In May 2005, it was officially announced that both games would be coming to the Nintendo DS as Mega Man Battle Network 5: Double Team DS,[21] although its existence was previously hinted at when Nintendo Power added an untitled Battle Network game to its release schedule.

[21] The DS version added additional content, including a new transformation for MegaMan called SolCross, unlocked by putting a copy of Boktai 2 into the GBA cartridge slot,[e] and being able to swap between Navis during fights.

[23][24] The developers had also experimented with fully 3D graphics early on, as 3D models of several areas and characters were found within the data of Mega Man Star Force,[25] although Christian Svennson, who served as Capcom's Vice President of Strategic Planning & Business Development, theorized in 2009 that the assets may have been made as a test of the DS' capabilities.

Mega Man Battle Network 5: Team Colonel placed at number 65 with 194,472 copies sold that year.

"[10] The Liberation Missions were also poorly received by reviews, with the general consensus being that they only slowed down the game;[10][11][6] GameSpy wrote that "Perhaps if the concept was fleshed out in a spin-off title, the experience would feel more complete than the "Final Fantasy Tactics for Dummies" vibe that it has now.