The USS Murgatroid's arrival was rather dramatic. Uncloaked, travelling at extremely high impulse speeds, she swung into the Solar System on a direct course to Earth. Having picked up a sort of cometary tail by passing through Jupiter's atmosphere, which was augmented and illuminated by various ship's systems, the Murgatroid was visible to the naked eye from Earth. She ignored all hails and challenges until she'd swung into a parking orbit around Earth. Once she'd arrived, she initiated a secure, scrambled connection with the Federation Council's building in San Francisco -- still refusing to speak to anyone else. All eyes were upon her, and everyone wondered what she was up to -- so nobody noticed Surak's Razor's
arrival on the moon...
The first people to whom Doctor Khan, acting captain of the Murgatroid, spoke were a bit intimidated. Khan, expressing a sense of extreme urgency without revealing any significant details, was able to bully his way up the chain of command -- he wanted to reach a certain minimum level of authority before he became bogged down in details. The fact that those in charge were also curious as to what exactly the Murgatroid was up to helped to speed Khan's ascension of the chain of command.
Nobody, however, reacted to the Murgatroid's arrival in quite the same was as
Janeway. Their surprise arrival, after claiming to be out in search of Lothar and Storvik, as well as their attempts to go over her head to the Federation Council, could only mean one thing -- they had come for her. She could tell that they were communicating with the Council's building on a secure channel, but had no way of monitoring the conversation. She knew, however, that it was about her. She didn't know what they had or what they knew; but they wouldn't have come after her, after feigning obedience, unless they thought that they had a winning hand. Janeway's plans had not progressed far enough that she could stop, stall, or deflect an inquiry; she still had to answer to those above her, and an inquiry would find evidence of her actions.
For one thing, she'd no longer be able to keep people from snooping around in her
torture chambers and laboratories in the sub-levels of Starfleet HQ. Up until now, she'd been able to prioritize, to assign the repair crews to the upper levels, the parts of the building visible to the outside world and accessible to the public. She had declared the sub-levels sealed off and too dangerous to enter -- although she still went in and out freely via transporters to continue questioning her prisoner, the real Admiral Kathryn Janeway of Starfleet, as well as to continue her researches and experiments. Her mental conditioning process still needed work, and she still sought control of Lothar and the GWIII Project responsible for his upgrades.
Janeway sent a coded signal to Voyager, a ship she had waiting on stand-by for her with a captive crew, to come in to transporter range of Earth to pick her up. She then had herself beamed down into her secret office in the sub-basement of the building. It was time to gather her files and destroy the rest before leaving...