Exhibit 99.3 INTERCREDITOR AGREEMENT This Intercreditor Agreement is made as of January 15, 2004 by and between WPV, Inc. (“Creditor”), and Comerica Bank (“Bank”). Recitals A. Scientific Learning Corporation (“Borrower”), has requested and/or obtained certain loans or other credit accommodations from Bank under a Loan and Security Agreement (the “Loan Agreement”) of even date, pursuant to which Borrower has granted Bank a security interest in the Collateral (as defined in the Loan Agreement). B. Creditor has caused to be issued for the benefit of Bank a StandbyLetter of Credit (the “Letter of Credit”) in support of Borrower’s obligations under the Loan Agreement. Borrower and Creditor are parties to a Reimbursement and Security Agreement (the “Reimbursement Agreement”) of even date pursuant to which Borrower agrees to reimburse Creditor for amounts paid in connection with the Letter of Credit, and secures its obligation under the Reimbursement Agreement with a security interest in the Collateral. C. Bank and Creditor desire to set forth their agreement with respect to the Collateral and certain other matters in this Agreement. NOW, THEREFORE, THE PARTIES AGREE AS FOLLOWS: 1. Bank consents to Borrower’s granting Creditor a security interest in the Collateral under the Reimbursement Agreement, provided such security interest secures only Borrower’s obligation to reimburse Creditor for any amounts owing to Creditor under the Reimbursement Agreement (the “Creditor Debt”). Creditor consents to Borrower’s granting Bank a security interest in the Collateral under the Loan Agreement, provided such security interest secures only Borrower’s obligation to repay the Obligations, as defined in the Loan Agreement (the “Bank Debt”). 2. Bank subordinates to Creditor any security interest or lien that Bank may have in the Collateral. Notwithstanding the respective dates of attachment or perfection of the security interest of Creditor and the security interest of Bank, the security interest of Creditor in the Collateral shall be prior to the security interest of Bank. 3. To the extent permitted under the California Uniform Commercial Code and all other applicable laws, upon the occurrence and during the continuance of an Event of Default under the Loan Agreement, Bank will draw on the Letter of Credit before exercising any remedies with respect to the Collateral. If any amount remains outstanding under the Loan Agreement after such drawing, then, notwithstanding Section 2 hereof, Bank’s security interest in the Collateral shall have priority over Creditor’s security interest in the Collateral, and Bank may exercise its rights under the Loan Agreement and applicable law, in whatever manner or order as Bank in its sole discretion may determine, until the Bank Debt has been satisfied in full. Upon repayment of the Bank Debt, the security interest granted to Creditor under the Reimbursement Agreement shall be a first priority security interest. Until the Bank Debt is paid in full, Creditor will not demand or receive from Borrower (and Borrower will not pay to Creditor) any amount, by way of payment, prepayment, setoff, lawsuit or otherwise in respect of the Creditor Debt, nor will Creditor exercise any remedy with respect to the Collateral, nor will Creditor commence, or cause to commence, prosecute or participate in any administrative, legal or equitable action against Borrower in respect of the Creditor Debt. Nothing in this Agreement shall affect the ability of any director of the Borrower, including any nominee of the Creditor or any affiliate of the Creditor, to perform its fiduciary duties as a director of the Borrower. Creditor shall promptly deliver to Bank in the form received (except for endorsement or assignment by Creditor where required by Bank) for application to the Bank Debt any payment, distribution, security or proceeds received by Creditor with respect to the Creditor Debt other than in accordance with this Agreement. 4. In the event of Borrower’s insolvency, reorganization or any case or proceeding under any bankruptcy or insolvency law or laws relating to the relief of debtors, these provisions shall remain in full force and effect.
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