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President Umaru Yar'Adua left Nigeria for medical treatment in Saudi Arabia in November 2009 without formally transferring power, and did not return for over two months, creating a constitutional crisis in which no one had clear authority to act as head of state while he remained critically ill.

The National Assembly passed a resolution in February 2010 invoking the 'doctrine of necessity' to make Jonathan, then Vice President, Acting President — a resolution outside the constitution's explicit text but broadly accepted as necessary. Yar'Adua died on 5 May 2010, and Jonathan was sworn in as substantive President the same day, resolving the vacuum.

Boko Haram emerged as an armed group in 2009 in Maiduguri, and its founder Mohammed Yusuf was killed extrajudicially in police custody in July 2009 after a failed uprising, driving the group underground and radicalising its remnants under new leadership.

Rather than being contained early, the group re-emerged with a bombing campaign from 2010 onward, escalating steadily through Jonathan's term into a full territorial insurgency by 2014-2015. The security services' initial handling of Yusuf's death was widely seen as having entrenched, rather than defused, the group's grievance narrative.

The 2008-09 global financial crisis exposed reckless lending and margin-loan exposure across Nigerian banks, and CBN Governor Sanusi Lamido Sanusi's 2009 intervention had removed several bank CEOs and injected emergency liquidity, but the sector's bad-debt overhang remained unresolved when Jonathan took over.

The Asset Management Corporation of Nigeria (AMCON) was established by an Act signed in July 2010 to acquire non-performing loans from the banking system, ultimately absorbing over ₦5 trillion in toxic assets and stabilising the sector's balance sheets over the following years.

The Yar'Adua administration's October 2009 amnesty had persuaded most militant groups to lay down arms, but the programme's stipends, training placements, and reintegration pipeline were still in an early, unproven stage, with real risk of relapse into violence if funding lapsed.

Jonathan, himself from the Niger Delta, continued and expanded the amnesty programme, keeping over 26,000 ex-militants on stipends and training placements. Major pipeline attacks and kidnappings fell sharply compared with the pre-2009 period for most of his term, though sporadic incidents continued.

The legal and regulatory framework for privatising the Power Holding Company of Nigeria had been enacted under Obasanjo in 2005 and partially advanced under Yar'Adua, but by 2010 the unbundled successor companies remained in government hands, with generation and distribution assets undercapitalised and poorly maintained.

Jonathan's administration completed the process, transferring 15 of the 17 unbundled PHCN successor companies to private core investors on 1 November 2013 — the most significant structural reform completed on his watch, even though it did not immediately translate into better supply.

The 2007 general election that first brought Yar'Adua to power was condemned by domestic and international observers as one of the least credible in Nigeria's history, marred by widespread rigging, violence, and low-quality logistics, leaving INEC's institutional credibility badly damaged.

Jonathan appointed Attahiru Jega, a respected academic and former ASUU president, as INEC chairman in 2010. Jega's INEC delivered the 2011 general election to broad international praise as the most credible since 1999, restoring significant institutional trust ahead of the 2015 handover.

Nigeria's petrol subsidy regime, already costly under Yar'Adua, continued to grow as an unbudgeted, off-balance-sheet drain on federation revenue, with limited transparency over who was actually receiving reimbursement for imported fuel.

Jonathan attempted a full removal in January 2012, but nationwide 'Occupy Nigeria' protests and a general strike forced a partial reversal within two weeks. A House of Representatives probe later that year found evidence of massive fraud in subsidy disbursement, but the underlying subsidy mechanism itself remained in place, largely unreformed, for the rest of the term.

Nigeria's GDP statistics were still calculated using a 1990 base year, failing to capture the growth of telecoms, entertainment, and services sectors that had emerged over the following two decades, meaning the country's true economic size was significantly understated in official figures inherited from prior administrations.

The National Bureau of Statistics rebased GDP to a 2010 base year in April 2014, nearly doubling measured GDP to roughly $510 billion and making Nigeria, by official statistics, Africa's largest economy ahead of South Africa.