one is a clearance, one is a flight plan
Straight from the Airmans Information Manual (AIM):
4-4-5. Special VFR Clearances
a. An ATC clearance must be obtained prior to operating within a Class B, Class C, Class D, or Class E surface area when the weather is less than that required for VFR flight. A VFR pilot may request and be given a clearance to enter, leave, or operate within most Class D and Class E surface areas and some Class B and Class C surface areas in special VFR conditions, traffic permitting, and providing such flight will not delay IFR operations. All special VFR flights must remain clear of clouds. The visibility requirements for special VFR aircraft (other than helicopters) are:
1. At least 1 statute mile flight visibility for operations within Class B, Class C, Class D, and Class E surface areas.
2. At least 1 statute mile ground visibility if taking off or landing. If ground visibility is not reported at that airport, the flight visibility must be at least 1 statute mile.
3. The restrictions in subparagraphs 1 and 2 do not apply to helicopters. Helicopters must remain clear of clouds and may operate in Class B, Class C, Class D, and Class E surface areas with less than 1 statute mile visibility.
b. When a control tower is located within the Class B, Class C, or Class D surface area, requests for clearances should be to the tower. In a Class E surface area, a clearance may be obtained from the nearest tower, FSS, or center.
c. It is not necessary to file a complete flight plan with the request for clearance, but pilots should state their intentions in sufficient detail to permit ATC to fit their flight into the traffic flow. The clearance will not contain a specific altitude as the pilot must remain clear of clouds. The controller may require the pilot to fly at or below a certain altitude due to other traffic, but the altitude specified will permit flight at or above the minimum safe altitude. In addition, at radar locations, flights may be vectored if necessary for control purposes or on pilot request.
NOTE-
The pilot is responsible for obstacle or terrain clearance.
REFERENCE-
14 CFR Section 91.119, Minimum safe altitudes: General..
d. Special VFR clearances are effective within Class B, Class C, Class D, and Class E surface areas only. ATC does not provide separation after an aircraft leaves the Class B, Class C, Class D, or Class E surface area on a special VFR clearance.
e. Special VFR operations by fixed-wing aircraft are prohibited in some Class B and Class C surface areas due to the volume of IFR traffic. A list of these Class B and Class C surface areas is contained in 14 CFR Part 91, Appendix D, Section 3. They are also depicted on sectional aeronautical charts.
f. ATC provides separation between Special VFR flights and between these flights and other IFR flights.
g. Special VFR operations by fixed-wing aircraft are prohibited between sunset and sunrise unless the pilot is instrument rated and the aircraft is equipped for IFR flight.
h. Pilots arriving or departing an uncontrolled airport that has automated weather broadcast capability (ASOS/AWOS) should monitor the broadcast frequency, advise the controller that they have the "one-minute weather" and state intentions prior to operating within the Class B, Class C, Class D, or Class E surface areas.
5-1-6. Flight Plan- Defense VFR (DVFR) Flights
VFR flights into a Coastal or Domestic ADIZ/DEWIZ are required to file DVFR flight plans for security purposes. Detailed ADIZ procedures are found in Section 6, National Security and Interception Procedures, of this chapter. (See 14 CFR Part 99.)
5-6-1. National Security
a. National security in the control of air traffic is governed by 14 CFR Part 99.
b. All aircraft entering domestic U.S. airspace from points outside must provide for identification prior to entry. To facilitate early aircraft identification of all aircraft in the vicinity of U.S. and international airspace boundaries, Air Defense Identification Zones (ADIZ) have been established.
REFERENCE-
AIM, ADIZ Boundaries and Designated Mountainous Areas,
Paragraph 5-6-5.
c. Operational requirements for aircraft operations associated with an ADIZ are as follows:
1. Flight Plan. Except as specified in subparagraphs d and e below, an IFR or DVFR flight plan must be filed with an appropriate aeronautical facility as follows:
(a) Generally, for all operations that enter an ADIZ.
(b) For operations that will enter or exit the U.S. and which will operate into, within or across the Contiguous U.S. ADIZ regardless of true airspeed.
(c) The flight plan must be filed before departure except for operations associated with the Alaskan ADIZ when the airport of departure has no facility for filing a flight plan, in which case the flight plan may be filed immediately after takeoff or when within range of the aeronautical facility.
2. Two-way Radio. For the majority of operations associated with an ADIZ, an operating two-way radio is required. See 14 CFR Section 99.1 for exceptions.
3. Transponder Requirements. Unless otherwise authorized by ATC, each aircraft conducting operations into, within, or across the Contiguous U.S. ADIZ must be equipped with an operable radar beacon transponder having altitude reporting capability (Mode C), and that transponder must be turned on and set to reply on the appropriate code or as assigned by ATC.
4. Position Reporting.
(a) For IFR flight. Normal IFR position reporting.
(b) For DVFR flights. The estimated time of ADIZ penetration must be filed with the aeronautical facility at least 15 minutes prior to penetration except for flight in the Alaskan ADIZ, in which case report prior to penetration.
(c) For inbound aircraft of foreign registry. The pilot must report to the aeronautical facility at least one hour prior to ADIZ penetration.
5. Aircraft Position Tolerances.
(a) Over land, the tolerance is within plus or minus five minutes from the estimated time over a reporting point or point of penetration and within 10 NM from the centerline of an intended track over an estimated reporting point or penetration point.
(b) Over water, the tolerance is plus or minus five minutes from the estimated time over a reporting point or point of penetration and within 20 NM from the centerline of the intended track over an estimated reporting point or point of penetration (to include the Aleutian Islands).
6. Land-Based ADIZ. Land-Based ADIZ are activated and deactivated over U.S. metropolitan areas as needed, with dimensions, activation dates and other relevant information disseminated via NOTAM.
(a) In addition to requirements outlined in subparagraphs c1 through c3, pilots operating within a Land-Based ADIZ must report landing or leaving the Land-Based ADIZ if flying too low for radar coverage.
(b) Pilots unable to comply with all requirements shall remain clear of Land-Based ADIZ. Pilots entering a Land-Based ADIZ without authorization or who fail to follow all requirements risk interception by military fighter aircraft.
d. Except when applicable under 14 CFR Section 99.7, 14 CFR Part 99 does not apply to aircraft operations:
1. Within the 48 contiguous states and the District of Columbia, or within the State of Alaska, and remains within 10 miles of the point of departure;
2. Over any island, or within three nautical miles of the coastline of any island, in the Hawaii ADIZ; or
3. Associated with any ADIZ other than the Contiguous U.S. ADIZ, when the aircraft true airspeed is less than 180 knots.
e. Authorizations to deviate from the requirements of Part 99 may also be granted by the ARTCC, on a local basis, for some operations associated with an ADIZ.
f. An airfiled VFR Flight Plan makes an aircraft subject to interception for positive identification when entering an ADIZ. Pilots are, therefore, urged to file the required DVFR flight plan either in person or by telephone prior to departure.
g. Special Security Instructions.
1. During defense emergency or air defense emergency conditions, additional special security instructions may be issued in accordance with the Security Control of Air Traffic and Air Navigation Aids (SCATANA) Plan.
2. Under the provisions of the SCATANA Plan, the military will direct the action to be taken-in regard to landing, grounding, diversion, or dispersal of aircraft and the control of air navigation aids in the defense of the U.S. during emergency conditions.
3. At the time a portion or all of SCATANA is implemented, ATC facilities will broadcast appropriate instructions received from the military over available ATC frequencies. Depending on instructions received from the military, VFR flights may be directed to land at the nearest available airport, and IFR flights will be expected to proceed as directed by ATC.
4. Pilots on the ground may be required to file a flight plan and obtain an approval (through FAA) prior to conducting flight operation.
5. In view of the above, all pilots should guard an ATC or FSS frequency at all times while conducting flight operations.