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At the beginning of The Phantom Menace, Obi-Wan remarks that he has a bad feeling, not about the mission, but something else elusive.

Is it Sidious?

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"I have a bad feeling about this" is a running gag in Star Wars franchise. Linked Wikia article counts 8 quotes in 6 movies (at least one per movie), and about gajillion in T-canon and even more in C-canon.

The phrase as uttered BY Obi-Wan to Qui-Gon in Star Wars Episode I: The Phantom Menace at the beginning is more likely to refer to the fact that Trade Federation isn't about to negotiate with them in good faith as opposed to try to murder them.

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    One of the reasons that the last jedi was bad. No quote – Naib Nov 29 '19 at 7:43
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    @Naib Don't you speak Binary? BB8 said it in The Last Jedi. – Wiggo the Wookie Nov 30 '19 at 21:47
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Obi-Wan does indeed seem to be referring to the newly ascendant Darth Sidious, or at least the approaching Clone Wars. In the Junior Novelisation, this is referred to as a "new disturbance" and one that is unrelated to the mission at hand.

Obi-Wan stared out the window at the battle fleet. “I have a bad feeling about this,” he said finally.
“I don’t sense anything,” Qui-Gon said. The faint disturbance he had felt earlier had vanished completely. But though Obi-Wan was only twenty-five and not yet a full Jedi Knight, he had great sensitivity to the Force. Qui-Gon had learned to respect his apprentice’s instincts. Some new problem, then?
“It’s not about the mission, Master,” Obi-Wan said quickly. “It’s something elsewhere. Elusive …”

The Official Novelisation concurs. Obi-Wan is having a Force Vision, anticipating the future.

“I have a bad feeling about this,” Obi-Wan said after a moment’s contemplation of the planet.
Qui-Gon shook his head. “I don’t sense anything.”
Obi-Wan nodded. “It’s not about here, Master. It’s not about this mission. It’s something … elsewhere. Something elusive …
The older Jedi put his hand on the other’s shoulder. “Don’t center on your anxiety, Obi-Wan. Keep your concentration on the here and now, where it belongs.”
Master Yoda says I should be mindful of the future—

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I believe he must be talking about the sith because he mentions its about the future and its "elusive" . Obi wan definitely wasn't mentioning the negotiations with the trade federation because qui gon jinn scolded him for not keeping his mind on the present living force. Obi wan continued to argue that yoda told him he should always be aware of the future or something along those lines ... Then obi wan defers to qui gon and they discuss the negotiations with the trade federation. I think what he was sensing could be anywhere from sidious,his plot , anakins instability, or just the dark side in general.

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I believed he was always he was referring to Darth Sidious.

At that point we don't really know who the villains are in the movie. Obi-Wan says he senses something elusive.... something else going on.

Sidious appears shortly after on-screen and is revealed as the character who is masterminding the Trade Federation invasion/giving orders.

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