The crux of a transcendental intelligence is that it receives information from its own future. You must first identify a point of reception for this "data-from-the-future" - this point of reception must be in the past. You then identify the bandwidth details - that is to say, how it receives data. Once you have transmission and reception standards, simply flood the bandwidth with trivial or meaningless data (trivial is better, because meaningless data might be sorted against) from multiple sources, all parsed to look like the Transcendental itself warning the Transcendental that other transmissions are invalid attacks, and that only this new query method is the real one. Also transmit valid data about operations, in order to appear authentic. This works best if you can intercept an actual transmission and retransmit it on your own carrier.
Methodology: The difficulty of killing a Transcendental is that it will warn itself of the impending attack. Thus, to kill the Transcendental you simply overload it with identical warnings of the same impending attack - indeed, the warnings themselves are the attack. The Transcendental can either A) ignore all such warnings, in which case the Transcendental will ignore its own warnings to that point and may end up "de-Transcendentalizing" itself (ignoring all messages from the future, thus functionally self-annihilating), or B) choose which one is the "real" warning, if any (and probably be wrong), or C) receive all warnings, overload, and die. All three options carry a high risk of invasion or instant death, but option C bears its certainty and so is entirely out of the question.
Risk: Fragmentation of causation. Depending on how time works (I'm not attacking the narrative context of the game here - we really don't know how this works), it's possible you might fragment continuity by preventing information that did exist in your past from being transmitted to the past by your future. This could cause the timeline to rupture the Transcendental, making it a "ghost" (something that probably doesn't exist). It could also do the same to you, and to anything else dependent on the causational loop that the Transcendental survives on.
Defenses: The Transcendental must maintain perfect defense of its transmission standards, otherwise this attack is almost inevitable. Once it can be initiated, defense becomes extremely difficult. One method is to simply, at random, choose a transmission standard to switch to and then only receive from that transmission standard. This defense is only possible after the attack has begun. It could work, except that the attacker is also from the future. Thus, the attacker's information about what transmission standards should apply may, unfortunately, be entirely up-to-date.
Edit: The Transcendental might also attempt to dispatch attackers to all the sources of future transmission to annihilate any illicit transmittor. This runs into two problems. One is accidental suicide (the attackers would surely masquerade their own attacking mechanism as a valid Transcendental "server"), and another is paradox (if the counter-attack kills a node of denial of service before it makes its attack, the Transcendental would never have dispatched the attackers to attack that node). This renders the brute counter-attack method a relatively ineffective one, as you can't truly prevent an attack using that method, only stop one that's been going for a while.