I recently watched again the episode of Deep Space Nine mentioned in the title. One gets the impression that in the end everything Sisko has done to get the Romulans into the war remains a secret. At one point Sisko asks Bashir to give him Bio-mimetic gel to which Bashir responds that he will file a complaint with Starfleet medical. If this is really such a controlled substance why were there no consequences to Sisko? (Which I assume there weren't since it was never mentioned again in further episodes.)
In short, the only people able to sanction Sisko for his illegal order are Starfleet. Since he's told them his plan, his order is actually (unbeknownst to Bashir) perfectly legal.
SISKO: It wasn't that funny. But I couldn't stop laughing. (beat) Maybe... I was under more pressure than I realized. Maybe it really was starting to get to me. (beat) At the time, I thought I was off the hook. Starfleet Command had given the plan their blessing and I thought that would make things easier.
Bio-memetic gel is restricted within the Federation because it's a vital component of biogenic weapons. The unique properties of the gel allow someone to target a specific genetic code, which is why it's used in both legitimate research and weapons which target specific bloodlines or species. Obviously, Dr. Bashir kept some on hand for the former. It's also a substance for which a little goes a long way, so eighty-five liters is quite a lot - far more than anyone would need for its legitimate use.
As for why Sisko faced no consequences, we never learn for sure. There are a few possibilities, however, and we have to assume that one of them is what happened:
- Garak, who had requested the gel, hacked the station's systems and erased the complaint
- Sisko, using his command-level clearance, circumvented or erased Bashir's complaint
- Sisko had the implicit (if not official) approval of his direct superior Admiral Ross
- Section 31 found out about what Sisko & Garak did and erased the complaint
I've listed them in order of most likely to least likely, but all are some variant of "Starfleet never found out". We have to assume that - had anyone with the authority learned about it - there definitely would have been consequences for Sisko, or at the very least we would have witnessed a tense conversation/confrontation between him and Admiral Ross.
I'd love to speculate about Section 31 and its nefarious dealings at Starfleet Command BUT I think an episode of TNG gives us the answer fairly clearly.
As previously stated, Sisko said Starfleet
had given the plan their blessing
Meaning, SOMEONE at SFC knew EVERYTHING Sisko had done and most of what Garak had done and was protecting Sisko.
This would not be the first time a cover up of this nature was mentioned on screen.
Pressman to Riker:
PRESSMAN: The Chief of Starfleet Security has personally assured me of her complete support.
Picard to Riker:
PICARD: The Judge Advocate also believes that the surviving officers are deliberately withholding vital information from this inquiry. Further investigation is recommended." (to Riker) But there was no further investigation... the file was classified and quietly buried.
Picard: ...It seems the file was sealed by Starfleet Intelligence.
So we KNOW that in extreme cases, Starfleet Intelligence will step in to cover up actions that might benefit the Federation but are of questionable legality. Bringing the Romulans into the war certainly benefits the Federation and Sisko's methods were definitely questionable (at best) in the legal sense of the term.