The Foot Headquarters in the 2003-2009 series, consists of various locations.
Oroku Saki Tower
The Oroku Saki Tower is the most used of all of the Foot headquarters and was the office, base, and central headquarters of Oroku Saki as the Utrom Shredder and was the office of his business. This base has been rebuilt at least twice. Both buildings were very similar in design, the tower included science labs, offices, quarters, a trap hallway, the Foot Mystics temple, a war room, and the main throne room. The tower also incorporated a hangar for air vehicles, a helicopter landing pad, and Japanese gardens. Above the Heliport was the Utrom Shredder's Shinto Palace. The building also had training facilities for the Foot Ninja.
Oroku Saki Mansion
The Oroku Saki Mansion is the second most used base in the TMNT 2003 series. Oroku Saki's mansion was a large spacious Japanese style mansion built as the base and home of the Utrom Shredder during season 3. It contained numerous labs, computer rooms, meeting rooms, training facilities, and even contained his spaceship and was the last known base the Utrom Shredder used before his exile in the season three finale "Exodus, Part 2".
At least one base in Japan had been seen in flashbacks as the Utrom Shredders base and was more like a palace for the Utrom Shredder and a training facility for Utrom Shredders forces too. This base is very large and was later headed by Karai until she came to New York City.
Alternate Future Base
The Utrom Shredder in an alternate future was ruler of the world and ruthless. He maintained a large palace that was guarded by Foot Police, Utrominators and Karai Legion. This palace held many valuables and was like a museum. The Utrom Shredder had a throne room where he would later be killed by Donatello.
The Utrom Shredder has had a base in a Foot owned boat and was a replica of Foot Tower design wise and incorporated Japanese style. It was here that the Foot Mechs were created and also where the Utrom Shredder was taking an absence from the Foot Clan to heal.
Shredders Warehouse base
In Ch'rell's first appearance as the Shredder in the 2003 series Utrom Shredder talked to Leonardo in a dojo style warehouse base that was designed for ninja training. It was here on the rooftop the Utrom Shredder and the Turtles had their first showdown.
Back To The Sewer Bases
In Back To The Sewer there were many bases used by the Foot, most were hi-tech training facilities in many different dojo's and warehouses, these bases incorporated both hologram and advanced technology. They were run and headed by Master Khan.
Khan had A Dojo that he trained and brainwashed people to be Foot minions. It was here he prepared for the Shredders' return.
In the special Turtles Forever, Ch'rell partners with the 1988 Shredder and Krang and the Technodrome becomes the headquarters for the 2003 TV series Foot Clan as well. After the apparent death of Ch'rell by being destroyed by the Technodrome's primary laser, the Technodrome returned to the 1988 Shredder and Krang and they returned to their own dimension. The 2003 Foot Clan presumably returned to Karai's leadership; their current headquarters is unknown.