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"So, there is another Navi who can wield Dr. Hikari's program..." ~ Serenade.EXE, MegaMan Battle Network 3
Giga Freeze was the name given to a hindrance program designed by Dr. Tadashi Hikari, the purpose of which being that it would be able to freeze Alpha in case its final seal, the Guardian Program, was destroyed. The program was so overwhelmingly powerful that one of the primary risks of its use was that, if it were mishandled, it could put the whole Internet into a permanent stasis. When Alpha was sealed, the program was hidden in the depths of the Undernet, under the care of Serenade, who proved to be a most effective guardian - he resided in one of the inmost regions of the Undernet, an area only privy to those who had access to the Undernet's server.
In MegaMan Battle Network 3, the Officials, via Chaud, commission Lan and MegaMan to seek out the program in the UnderNet, known to be with a Navi operating under the name "S". The quickest way to find "S" was to encounter him as the top-ranked Navi of the Undernet, and thus they were asked to join a competition called the Ranking. To do so, the Hikari brothers traveled to the Under Square, the Undernet's rendition of the public forums becoming more and more popular on the surface Internet.
After defeating the Navi with Rank 2, (MistMan.EXE / BowlMan.EXE), Lan and MegaMan were given a clue as to where "S", now known as Serenade, could be found - in a secret area "hidden by a boulder". Following this, the Hikari brothers discovered the mysterious location - at the Ura Inn in Yoka, they discovered a secret elevator hidden in the rock face of the Inn's hot-spring fountain, which led them to the nothing less than the server of the Undernet, which led them to a secret area of the Under Square, where they encountered Serenade, who spoke to them from the other side of a large, white hole (a sealed portal) directly in front of where MegaMan emerged.
MegaMan immediately asked for Serenade to give him the Giga Freeze so that they could use it to stop Alpha in case it was awakened. Unfortunately, as Serenade immediately pointed out, the program was not able to be passed around freely between NetNavis for fear of them falling victim to the Giga Freeze's power. Instead, the program was only able to be wielded by designated users, "Chosen Ones", and if MegaMan really wanted the program, he would have to undergo a "test" to see if he could wield it. The test in question was that Serenade would give the program to MegaMan - if MegaMan was indeed the Chosen One, he would be able to leave with it in his position, free to wield it. If he was not, the program would activate and he would be frozen for eternity. In the hands of a Chosen One, the Giga Freeze would burst into flame, the lack of this flame indicated that the Navi undergoing the test had failed and was now frozen. Undeterred, MegaMan underwent the test, and grasped the program Serenade summoned before him. When nothing happened, Lan began to cry MegaMan's name in fear, and even Serenade seemed to believe that MegaMan had been frozen, when the program burst into flame before them. Now delighted, Serenade informed MegaMan that he was free to wield the program, and Lan jacked his Navi out, leaving Serenade to muse that another Navi (MegaMan) could wield Dr. Hikari's program, suggesting that Serenade knew of other Navis capable of doing so.
Meanwhile, MegaMan immediately decided that they should turn the program over to the Officials as per their agreement, when they are distracted by none other than Mamoru, a sickly child who Lan and MegaMan had earlier inspired to undergo heart surgery, who gives them some insight into the history of the Undernet, especially how it was designed by his father, a SciLab employee, specifically for the purpose of housing the Giga Freeze program, which was too dangerous to hide away in any other way. After learning this, the Hikari brothers are interrupted by a warning siren: the Undernet's server room, though distinct from the SciLabs proper, was still connected to it, so Lan and MegaMan were present for the alert that an unknown Navi had broken into the SciLab Area, and had broken through Alpha's containment area. MegaMan is sent to chase down the thief, WWW Navi Drillman, and discovers him at the end of an Undernet pathway after travelling through a hole in the very fabric of the Internet.
Upon defeating the thief, Lan and MegaMan find the cell containing Alpha where DrillMan was once standing, and move to reclaim it, when they are interrupted by none other than Bass.EXE, the phenomenally powerful NetNavi who had nearly deleted MegaMan during their last encounter. Apparently working with Wily, who had called him back before he could finish MegaMan off previously, Bass took Alpha's holding cell with the intention of delivering it, as DrillMan was no longer able to. In desperation to prevent this, MegaMan hurled the full force of the activated Giga Freeze program at Bass. Blinded by the attack, Lan wondered aloud if they had succeeded in preventing Bass, only for them to discover to their shock that Bass had caught the attack in his spare hand.
MegaMan was horrified all the more, wondering if Bass was another Chosen One like him, whereas Bass himself found the situation rather interesting, demonstrating that he had known of the GigaFreeze, though had obviously not expected it to be in MegaMan's hands. Impressed, he again decided to let MegaMan live, warping away with a flick of his cape, leaving the Hikari brothers to deliver the bad news to the Officials.
It is unknown what happened to the program since the encounter between MegaMan and Bass. While later examination has revealed that the main program was still in Lan's and MegaMan's possession, it is unknown whether it still had its power, as it is never made clear what exactly happened to the Giga Freeze after Bass caught it: Bass did not use its power during his next confrontation, but neither did MegaMan use it against Alpha in the moments afterward, instead doing battle with it after its awakening (which would theoretically have been the proper moment to use the program). Also unknown is whether or not, when Serenade was musing to himself over the existence of others with the ability to wield the Giga Freeze, whether he was simply referring to himself or if he had known of Bass' ability to do so. Serenade himself gives no answer, demonstrating no concern for the Giga Freeze when he appears to MegaMan, though he does say that he has battled with a NetNavi heavily implied to be Bass in the past.
The Giga Freeze also appears in Ryo Takamisaki's manga, Megaman NT Warrior. In this incarnation, it is wielded by the powerful Navi, Colonel.EXE, who uses it in his opening appearance to obliterate the realm of the Darkloids, where MegaMan, ProtoMan, SearchMan, and (to a certain extent) BubbleMan have been fighting.The Giga Freeze appears when Colonel, having just called off his associate Tomahawkman's (surprisingly effective) attack on the Darkloid hordes, draws his arms back and something powerful and bright begins to charge behind him. His short conversation with MegaMan implies that the attack he's summoning will be the finishing blow, and MegaMan can only wonder if his attack is pure light when Colonel unleashes the Giga Freeze, a blinding wave of energy so powerful that it not only wipes out the Darkloids, but when MegaMan opens his eyes again, he sees the actual Internet around him again, as if the Dark World itself had been torn away.
No explanation is given as to the mysterious power Colonel wields in his opening appearance, though it is only used once in his entire run during the comic. Its sole use is never given thought after the fact except once when MegaMan reflects on Colonel's power, so there is no way of telling whether it was a blast from a program, like TomahawkMan's Anti-Dark Power program, or if it was one of Colonel's natural abilities, though the lack of its repetition suggests the first option.
The Giga Freeze's function seems to vary greatly in its appearances. In the games, its sole function is to freeze whatever program it is used on, even something as powerful as the primordial internet program, Alpha. There is only one symptom of its use: the program mishandling it will have ceased functioning; when MegaMan accepts the program from Serenade, Serenade draws his conclusion from MegaMan's lack of motion. In Takamisaki's manga, however, the Giga Freeze unleashes a wave of destruction that is particularly potent against Dark Power, though it is never explicitly stated that the Giga Freeze in the manga has a different function than it does in Battle Network 3 - indeed, Colonel uses the power in order to "seal up the Big Dark Hole - for good." However, the games make the explicit point that only a Chosen One can wield the power of the Giga Freeze properly; it is unknown whether this implies that the wielder must be sufficiently powerful or have a specific type of code in their program, though the implication is that it is not a matter of strength. It is not established what this means for Colonel.
The Giga Freeze's separate incarnations, while no attempt is really made to establish similarity besides name, do share one quality: their usage is heralded by a blinding, all-enveloping light. It is unknown if the light is either the form of the attack, or merely its byproduct; the game suggests that it is the latter, as the Giga Freeze's power itself is concentrated in the glowing orb that MegaMan throws at Bass, while the manga makes a point of establishing the Giga Freeze's brightness, to the point where the wave that Colonel summons seems to invert and destroy the Dark World itself.