A technical plan was prepared to modify a Project 667A strategic missile submarine cruiser into a Project 09780 sub (‘Akson-2’) for sea trials of sonar systems for the new generation of submarines. Chief Designers were O.Ya. Margolin and E.A. Gorigledjan from 1987. Later, Rubin's suggestion was accepted that the Project 667AK submarine (Akson-1) was to be refitted to Project 09780 after completion of its testing program to reduce the cost and duration of refitting. The revised technical plan for refitting that submarine to Project 09780 was developed in 1988. The scope of works within Project 09780 was considerably wider as compared to 667AK not only because antennas became much larger and the equipment amount increased, but also because of the very strict requirements from the sonar to interference, power supply and cooling. In the process of refitting, a number of engineering problems found their solutions crucial both for the production of a new generation prototype submarine and serial boats. The works on the submarine refitting and repair were completed in August 1995. After successful Harbour Tests, Shipyard Sea Trials and State Acceptance Trials the submarine was commissioned by the Navy in 1996.
The company received a new name – Central Design Bureau for Marine Engineering ‘Rubin’ (CDB ME ‘Rubin’) - since the scope of its services was extended.
The first Russian tourist submarine Neptun was built to the design by Rubin.
The tourist submarine Sadko was built to the design by Rubin.
The company changed its official name to the Federal State-Owned Unitary Enterprise ‘Central Design Bureau for Marine Engineering ‘Rubin’ (FSUE ‘CDB ME ‘Rubin’).
The first commercial launch was done from the floating launch facility within the Sea Launch international project. Rubin was involved in the creation of the Assembly and Command Ship and Launch Platform meant for space craft launches. Rubin was commissioned for the project to provide the marine use of the equipment previously used only for launching rockets from land-based space launching sites.
The International Russian-Dutch Consortium finished the recovery of the sunken Kursk, a Project 949A nuclear submarine cruiser. The operation had had no parallels in the world practice. Rubin was in charge of planning the recovery operations.
The first Russian high-speed electric train was built to the design by Rubin.
V.A. Zdornov was appointed Director General of CDB ME "Rubin" to be at the head of the company until 2009.
CDB ME ‘Rubin’ was reorganized into Public Joint-Stock Company ‘Central Design Bureau for Marine Engineering ‘Rubin’ (OAO ‘CDB ME ‘Rubin’).
A.A. Dyachkov, who had been Head of the company up until 2012, was elected Director General of CDB ME Rubin at a special meeting of shareholders.
The Saint Petersburg non-nuclear submarine of the IV generation Project 677 designed by Rubin was commissioned by the Navy.