SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 -------------- SCHEDULE 13D/A (RULE 13D-101) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULE 13D-1(a) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13D-2(a) (Amendment No.1) INTERCEPT, INC. ----------------------------------------------------------------------- (Name of Issuer) COMMON STOCK ----------------------------------------------------------------------- (Title of Class of Securities) 45845L107 ----------------------------------------------------------------------- (CUSIP Number) Marc Weingarten, Esq. SCHULTE ROTH & ZABEL LLP 919 Third Avenue New York, New York 10022 (212) 756-2000 ----------------------------------------------------------------------- (Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications) April 26, 2004 ----------------------------------------------------------------------- (Date of Event Which Requires Filing of This Statement) If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of Rule 13d-1(e), 13d-1(f) or 13d-1(g), check the following box |_|. NOTE. Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. SEE Rule 13d-7 for other parties to whom copies are to be sent. -------- 1 The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page. The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, SEE the NOTES). (page 1 of 6 pages) ------------------ --------------- ------------------ CUSIP No. 45845L107 13D Page 2 of 6 Pages ------------------ --------------- ------------------ ======================================================================= 1 NAME OF REPORTING PERSONS I.R.S. IDENTIFICATION NOS. OF ABOVE PERSONS (ENTITIES ONLY) JANA PARTNERS LLC ----------------------------------------------------------------------- 2 CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP* (a) |_| (b) |_| ----------------------------------------------------------------------- 3 SEC USE ONLY ----------------------------------------------------------------------- 4 SOURCE OF FUNDS* WC ----------------------------------------------------------------------- 5 CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEM 2(d) OR 2(e) |-| ----------------------------------------------------------------------- 6 CITIZENSHIP OR PLACE OF ORGANIZATION DELAWARE ----------------------------------------------------------------------- NUMBER OF 7 SOLE VOTING POWER SHARES BENEFICIALLY 1,639,937 OWNED BY EACH REPORTING PERSON WITH -------------------------------------------------------- 8 SHARED VOTING POWER -0- -------------------------------------------------------- 9 SOLE DISPOSITIVE POWER 1,639,937 -------------------------------------------------------- 10 SHARED DISPOSITIVE POWER -0- -------------------------------------------------------- 11 AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON 1,639,937 ----------------------------------------------------------------------- 12 CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES* |_| ----------------------------------------------------------------------- 13 PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11) 8.10% ----------------------------------------------------------------------- 14 TYPE OF REPORTING PERSON* IA =================================================================== SEE INSTRUCTIONS BEFORE FILLING OUT!* ---------------------------------- ------------------ --------------- ------------------ CUSIP No. 45845L107 13D Page 3 of 6 Pages ------------------ --------------- ------------------ The Schedule 13D filed on April 12, 2004 (the "Schedule 13D") by Jana Partners LLC, a Delaware limited liability company (the "Reporting Person"), relating to the common stock, no par value (the "Shares"), of InterCept, Inc. (the "Issuer" or "InterCept"), is hereby amended and supplemented as set forth below by this Amendment No. 1 to the Schedule 13D. Item 3. Source and Amount of Funds or Other Consideration. ------------------------------------------------- Item 3 of the Schedule 13D is hereby amended and restated in its entirety as follows: The aggregate purchase price of the 1,639,937 Shares of Common Stock owned beneficially by JANA Partners LLC is $19,830,617. Such Shares of Common Stock were acquired with investment funds in accounts under management. Item 4. Purpose of Transaction. ---------------------- Item 4 of the Schedule 13D is hereby supplemented as follows: On April 26, 2004, the Reporting Person announced that it had filed a counterclaim for injunctive and declaratory relief in Georgia federal court to force the Issuer to comply with its longstanding bylaw provision requiring the election of four directors to the Issuer's Board of Directors at its 2004 Annual Meeting. In its court filing, the Reporting Person also seeks alternative relief to bring other proposals to a vote at the Annual Meeting. The Reporting Person is also seeking the court to force the Issuer to turn over all of the information to the Reporting Person that it is entitled to under Georgia law in order to effectively communicate with its fellow shareholders in connection with the Annual Meeting. More information is available in the Reporting Person's April 26, 2004 letter to John W. Collins, Chairman and Chief Executive Officer of the Issuer, and the Reporting Person's April 26, 2004 press release, copies of which are attached as exhibits hereto. Item 5. Interest in Securities of the Issuer. ------------------------------------ Item 5(a) of the Schedule 13D is hereby amended and restated in its entirety as follows: (a) The aggregate percentage of Shares of Common Stock reported owned beneficially by the Reporting Person is based upon 20,253,980 Shares outstanding, which is the total number of Shares of Common Stock outstanding as reported in the Issuer's Annual Report on Form 10-K for the year ended December 31, 2003. As of the close of business on April 12, 2004, JANA Partners LLC beneficially owned 1,639,937 Shares of Common Stock, constituting approximately 8.1% of the Shares outstanding. ---------------------------------- ------------------ CUSIP No. 45845L107 13D Page 4 of 6 Pages ---------------------------------- ------------------ Item 7. Material to be Filed as Exhibits. -------------------------------- Item 7 is hereby supplemented as follows: Attached hereto as Exhibit 2 is a Letter, dated April 26, 2004, to John W. Collins, Chairman and Chief Executive Officer of InterCept, Inc. Attached hereto as Exhibit 3 is a press release, dated April 26, 2004. ------------------ ------------------ CUSIP No. 45845L107 13D Page 5 of 6 Pages ------------------ ------------------ SIGNATURES After reasonable inquiry and to the best of its knowledge and belief, the undersigned certifies that the information set forth in this statement is true, complete and correct. Dated: April 27, 2004 JANA PARTNERS LLC By: /s/ Barry S. Rosenstein ------------------- Barry S. Rosenstein Managing Director By: /s/ Gary Claar ------------------- Gary Claar Managing Director ------------------ ------------------ CUSIP No. 45845L107 13D Page 6 of 6 Pages ------------------ ------------------ SCHEDULE A Schedule A of the Schedule 13D is hereby amended and restated in its entirety as follows: Transactions in the Shares During the Past 60 Days -------------------------------------------------- Shares of Common Stock Price Per Date of Purchased (Sold) Share($) Purchase (Sale) ----------- --------- ------------- 218,610 12.3390 03/10/04 160,000 12.7084 03/11/04 50,000 12.4533 03/12/04 80,000 11.9757 03/15/04 67,600 11.4782 03/23/04 201,027 10.7546 03/24/04 50,000 10.8500 03/25/04 112,700 11.6988 03/30/04 95,400 12.0020 03/31/04 176,200 12.2856 04/01/04 173,900 12.4782 04/02/04 150,500 12.4860 04/05/04 84,000 12.8200 04/07/04 20,000 12.9000 04/12/04