The following is my attempt to explain why Baltar did what he did, and frame it in the background of the classic program. It also explains that green outfit John Colicos wore in character, beginning in Lost Planet Of The Gods, and why he did not wear it before then. Finally, it reveals Baltar's fate.
This is not strictly canon as yet. What it is, instead, is my personal speculation, so I ask your indulgence for that.
The Colonial Merchant Marine And The Motive Of Baltar's Treason
Part One: The Colonial Merchant Marine
Along with the rise of the Colonial Service went the rise of the Colonial Merchant Marine. An alliance of traders who also had a measure of military training, it used an essentially similar command structure to the Colonial Service; Baltar was the last Commander of the Colonial Merchant Marine. However, unlike the Colonial Service's battlestars, Colonial Merchant Marine ships had no Vipers, or other such combat-oriented small craft, and relied on banks of turret-mounted laser cannons to defend their most vital areas from attack. Also unlike battlestars, Merchant Marine ships had no launch platforms for space-to-space torpedoes.
There was enough lawlessness where the traders plied their trade for fighting and scars to be part of their overhead. Their vessels, more than half of which were freighters, did not have to worry that much about Cylons, but they were in frequent danger of piracy, and they faced fierce competition from smuggling. Indeed, some Colonal Merchant Mariners actually turned smuggler and/or pirate, and were able to evade their former compatriots's protective measures. Inevitably, the Colonial Merchant Marine gained a high degree of economic control of the Colonies. Its best traders grew rich, and with riches came political power. Many Colonial Merchant Marine Commanders were able to cause themselves to be elected to the Quorum/Council Of The Twelve; Baltar himself was perhaps the most prominent example of this.
Colonial Merchant Marine personnel tended to wear green uniforms with tan suede boots, sometimes adorned with long green dress capes. Like Warriors in the Colonial Service, "Hagglers" in the Colonial Merchant Marine attended an academy to win licenses for their duties. Baltar was a highly respected figure in the Colonial Merchant Marine even before he became its last Commander, for he showed an uncanny knack for both achievement and survival. Indeed, when he attained to the age of sixty-five yahrens, he became the youngest Commander in Colonial Merchant Marine history and, with a tenure of thirty-five yahrens before he committed his treason, its longest-tenured ever.
Then he committed his treason.
Part Two: The Motive Of Baltar's Treason
In the thirty-first yahren of Baltar's tenure as the Commander of the Colonial Merchant Marine, reasoned as both Yahren 6566 and Yahren 7338 by Colonial calendars, he recruited a personal pilot and electronics engineer named Charybdis. It was under the code name Proteus that the Colonial Service came to know of Charybdis. A treacherous and untrustworthy individual, he would later murder the Colonial Warrior Ensign Ortega aboard the Rising Star, which had once been Commander Baltar's flagship. Baltar never trusted Charybdis fully, and even grew to hate him, but eventually he found himself unable to do without him. He ended up practicing the wisdom of keeping one's friends close--and one's enemies closer still.
As has previously been stated, the Colonial Merchant Marine's ships were in frequent danger of piracy and also faced fierce competition from smuggling. Charybdis, who had become as dependent on Baltar as Baltar was on him, hated this interdependency and longed to strike out on his own. In Yahren 6567, which was also Yahren 7339, Charybdis learned that Baltar had acquired massive stores of Tylium, solium, petro, and solonite--the three fuels and the explosive without which neither the Colonial Service nor the Colonial Merchant Marine could do. Hoping to overthrow Baltar as Commander of the Colonial Merchant Marine, he revealed the locations of all four to the ringleader of the cruelest and most ruthless piracy and smuggling ring then menacing Colonial Merchant Marine shipping, a man Baltar personally knew--and hated. Charybdis did more, and worse. He revealed how to evade the security precautions Baltar had taken with it all.
The pirate-smuggler wasted no time in taking evil advantage of Charybdis's treachery against Baltar. He and his ring raided the private storage containers of his enemy and stole all the Tylium, all the solium, all the petro, and all the solonite. Shocked, horrified, and enraged to find his most valuable cargo gone, Baltar gathered up every cubit he had available, including some that served as "tracer" cubits, and commenced, aboard his flagship, the Rising Star, to track down his enemy and his cargo. There, he began trade negotiations, using the Haggling skills he had learned in the Colonial Merchant Marine Academy, hoping to buy back his stolen cargo. He had to do so without Charybdis, of whose role in that crime he remained ignorant for yahrens, learning of it only when Charybdis stood tribunal for Ortega's murder, for which he had already framed the Colonial Warrior Lieutenant Starbuck, and of which crimes Charybdis was eventually convicted.
Unfortunately for Baltar, he was far from alone in wanting the ringleader pirate-smuggler caught and brought to justice. The Colonial Service was already also in hot pursuit of that unworthy, a pursuit that the Colonial Service's Commander, Commander Adama, Commander of the Colonial Service battlestar Galactica and the son of the legendary Commander Theo, who had likewise commanded both the Galactica and the Colonial Service, had initiated. To Adama, there were too many irregularities involved in the trade negotiations Baltar was pursuing, and he was convinced he had to bring a stop to them before something clearly illegal resulted.
The Galactica caught up with the Rising Star just as the negotiations were reaching a critical point. Adama ordered three of his best Warriors, Lieutenant Apollo and Ensigns Boomer and Starbuck, to intercept the ringleader pirate-smuggler's ship and board it. Leaving the bridge of the Galactica in the hands of Major Tigh, whose own poor restraint of his emotions had already cost him at least one command of his own, Adama came on board the other ship along with Apollo, and the four Colonial Service personnel broke up the deal before it could be closed. As the Colonial Service was facing a fuel and munitions shortage of its own at the time, Adama ordered the cargo impounded, and Baltar's cubits seized, as evidence in the eventual tribunal, in which the ringleader pirate-smuggler was convicted of all charges. But over Adama's objections, Adar, the then President of the Quorum/Council Of The Twelve, refused to allow Baltar to be repaid a single ducat of the thousands of millions of cubits he had tried to invest in recovering the cargo.
The results were disastrous for Baltar and, eventually, for the Colonies.
For what should have been the greatest mercantile triumph of Baltar's career instead became his most ignominious economic disaster.
Forced to close down the Colonial Merchant Marine Headquarters on his native Canceria, whose building had also been his personal home, because he could no longer afford to care for it, Baltar was left financially impoverished, with hundreds of millions of cubits in personal debt, though he still retained his seat on the Quorum/Council Of The Twelve. So homeless was he rendered, in fact, that he had to sell the Rising Star, for ducats on the cubit, to a Leo sire by the name of Uri to cover the worst of his debts. Moreover, so that he might even have a ship of his own, Baltar was forced to salvage and restore an abandoned, derelict garbage scow, then convert it. The entire Colonial Merchant Marine was thus forced to conduct its operations at a severe financial loss, not mitigated in the least by the fact that a third of its ships had already been destroyed, or that many of its best Hagglers and traders had been killed, by the pirates and smugglers whose ringleader Baltar had tried to deal with to get his cargo back.
Baltar blamed Adama for the loss of his home and the reversal of his fortunes, and swore revenge. It took him three yahrens to find a way to get that--a means of depriving Adama of his home and reversing his fortunes--but eventually he did. It occurred to him that maybe the Cylons would give him at least a home, where he might be able to subjugate some humans. But if he was to get that, then he would have to do something that would have been completely unthinkable to him before this--betray the Colonies to the Cylons.
He stopped wearing his Colonial Merchant Marine uniform and took to wearing civilian clothing. Using his Haggling skills, he communicated with the Imperious Leader of the Cylons, relying on Charybdis to maintain open channels. At first his proposal drew skepticism from the Imperious Leader, who had functioned for a thousand yahrens. Over time, however, Baltar was able to convince the Imperious Leader to follow his plan. He did not count on the Imperious Leader being willing to order him executed upon being convinced that his usefulness to the Cylons had seemingly ended, which that particular Imperious Leader would not function long enough to do. Nor did he count on that Imperious Leader, whose bargain with Baltar called for Canceria to be spared, altering the bargain and claiming that Baltar had missed the entire point of the war.
When the Imperious Leader with whom Baltar had dealt was destroyed before Baltar could be publicly executed, his successor, who had an identical voice to his predecessor, proved to be more flexible, and even gave him a base star to command, thereby making him an organic warlord amongst a race of machines. This enabled Baltar to pursue his revenge plans against Adama. Of course, by then, there was no more Colonial Merchant Marine, but Baltar still, regardless, resumed wearing his Colonial Merchant Marine uniform.
Ultimately, Baltar finally received a conviction for his treason in a tribunal and judgment from a more recent roster of the Quorum/Council Of The Twelve. (This was thanks to the personal intervention of the evil Count Iblis. Yahrens before, Count Iblis had deceived the original reptilian Cylons into creating their robotic armed forces; these had ultimately turned on, and destroyed, their own creators. Count Iblis's voice became that shared by all the Imperious Leaders of the robotic Cylons.) After receiving that judgment and being confined to the prison barge of the Galactican ragtag fleet, Baltar was marooned on an inhabited planet, where he eventually died.