The whole ordeal with Jedi Shaak Ti, mostly played by actress/model Orli Shoshan, is a long and rough story to tell. It's actually told best by someone who was actually on the sets when her scenes were filmed. That man would be Pablo Hidalgo who writes about this character's scenes in glorious detail at Starwars.com which you can read by clicking here. Unfortunately, at the time I'm writing this, you have to actually PAY to read this information there so if you're not a member of the fan club or have access to the pay service, the link I'm supplying will mean nothing to you and there's not much more I can do to help you get the info you seek. Were I to post the images or text from that page, they'd send their lawyers after me, but that's another story... I'll do my best to give you what information I can here.
Shaak Ti was actually cut from EPISODE III twice, if you can believe that. Once from the Sydney shoot where she had a fateful meeting with General Grievous, and once from the Shepperton pickups where she died at the hands of fallen Jedi, Anakin Skywalker, during the Jedi Temple slaughters. In fact, the first mention of her was to take place during the opening space battle. Apparently, Shaak Ti was one of the Jedi responsible for protecting the Chancellor and last they heard, she was still with him. That means she was aboard Grievous' ship. The two exchanged the following lines in the original script:
ANAKIN
The last message we had from
Master Shaak Ti, she was still
with the Chancellor.OBI-WAN
She's the most cunning of Jedi.
She's even shown me a few tricks.
They won't catch her.ANAKIN
Artoo, trace Shaak Ti's
homing signal!
This whole subplot was interwoven with the Clone Wars cartoon series on Cartoon Network. The episodes showed a valiant Shaak Ti try to protect and defend the Chancellor from the clutches of General Grievous, who ultimately prevails with his prey. In the cartoons, however, Shaak Ti doesn't make it to Grievous' flagship nor does she die.
According to the EPISODE III text above, however, she makes it up there just fine, most likely as a second captive, next to the Chancellor. It's there that she meets her originally scripted demise, at the hands of Grievous. In fact, she dies right before the eyes of Anakin and Obi-Wan who happen to be on their way to find the Chancellor. They come across her in a hallway, sitting quietly on the floor. Grievous is there and decides its time to teach this Jedi a lesson. According to Starwars.com, his line (as it was read on the set the day of filming) went like this, "Shaak Ti, your lightsaber seems a little battle-worn. It will need considerable cleaning, but it will do the job." Then he killed her with her own lightsaber, Bon Jovi style - through the heart.
There were internet rumors long before the film came out (originating at AICN, I believe) that Grievous was supposed to behead Shaak Ti but I've found no evidence of this in any printed materials. That's not to say it was never considered, I just don't have any evidence of it to share with you.
The way it's supposed to happen is that the Jedi are making their way through the ship, come across Shaak Ti, witness her murder, become grim, realize they are outnumbered and then cut their way through the floor to escape Grievous and his droids, which leads into another cut scene discussed here. One of the images below from The Making of Revenge of the Sith brings us through that sequence. Another shows what the scene might have looked like using the actor and a digital Grievous.
At some point, Lucas decided that the opening scenes were running a little too long so he cut out a lot of the opening hijinks that occur on Grievous' flagship. The death of Shaak Ti was one of those cuts and the mentions of her beforehand were all removed to cover the tracks.
During pickup shooting in September 2004, Orli Shoshan was flown from Australia to Shepperton Studios in London to give it another go as Shaak Ti. The scene was short and all she had to do was sit on a cushion, wait for Anakin to walk in, say the line, "What is it, Skywalker?" and then die the same way she did it months prior - Bon Jovi style. This was shot but never made it into the film. There's a picture below from The Making of Revenge of the Sith and here's the only remaining evidence from the published screenplay:
144 INT. CORUSCANT-JEDI TEMPLE-NIGHT
ANAKIN walks through the Jedi Temple, where he finds and kills SHAAK TI. He exits Shaak Ti's room and enters a hallway, where the battle is taking place.
It's possible that a shot from the animatic version of the EPISODE III trailer of Anakin walking could have been the next shot mentioned where Anakin walks into a hallway where the battle is taking place, but it's hard to say for sure.
The shots of Grievous killing Shaak Ti are available on the EPISODE III DVD. They segue into the fuel tank sequence also, so it's almost like getting two cut scenes for the price of one. Check them out when you can.