By John R. Ellement, Globe Staff

A person was struck and killed this afternoon by an MBTA commuter rail train near where tracks cross Cabot Street in Beverly, according to the MBTA and the Massachusetts Bay Commuter Railroad Co.

An inbound train “struck a trespasser just east of the Cabot Street’’ around 12:30 p.m., according to a statement from the private company that operates the commuter rail. About 150 passengers were on board the Newburyport/Rockport train, which left the station around 12:10 p.m.

By Jasper Craven, Melissa Hanson and Martin Finucane, Globe Correspondents and Globe Staff

The National Weather Service issued tornado warnings this afternoon for various areas as a parade of strong thunderstorms marched northeast across Massachusetts. As of 3 p.m. a tornado warning remained in effect for Essex County. Forecasters advised people to take cover in a basement or an interior room on the lowest floor of a sturdy building. An earlier warning had covered areas of Essex, Worcester, and Middlesex counties, but it has now expired.

By Brian Ballou and John R. Ellement, Globe Staff

A Boston man allegedly was sexually assaulting an unconscious woman early Sunday morning when State Police appeared near the Community Boating area on the Esplanade and forced him to stop his attack, according to a State Police report filed in court today. Joseph Barthel, 49, pleaded not guilty to an indecent assault and battery charge in Charlestown Municipal Court. Judge Robert McKenna set bail at $100,000 cash. Barthel, who was listed as living at the New England Shelter for Homeless Veterans, is due back in court Aug. 2.

By Colin A. Young, Globe Staff

A new pyrotechnics company, a reconfiguration of the barges on the Charles River, and pyrotechnics fired from the Massachusetts Avenue bridge will all contribute to a fireworks display like no other on the Fourth of July in Boston, event organizers said today. Promising “basically every firework shell you’ve ever seen,” pyrotechnics show producer Matt Shea said this year’s show will include about 16,000 different fireworks.

By Michael Levenson, Globe Staff

House and Senate lawmakers are preparing to give final approval today to a $34 billion spending plan that includes an increase in funding for the University of Massachusetts system and new measures to crack down on welfare fraud. Legislative negotiators reached agreement on the budget on Sunday night and expect to send it to Governor Deval Patrick today, when the new fiscal year begins. Patrick has not indicated whether he will sign the plan or send it back with changes.

By Milton J. Valencia and Shelley Murphy, Globe Staff

Disgraced former FBI agent John Morris grew emotional on the stand in the trial of James “Whitey” Bulger Monday as he looked at the family of one of the gangster’s alleged murder victims and apologized for what he has acknowledged could have been his “indirect” role in the killing. “Not a day goes by that I don’t pray that God gives you blessing and comfort for the pain,” Morris said to the Donahue family, seated in the front row.

By John R. Ellement, Globe Staff

The body of a man in his 50s was found in Ronan Park in Dorchester today and Boston police are investigating his death as a probable suicide, police said. Police said a woman called around 5:15 a.m. today and reported seeing what she believed to be a body in Ronan Park. Responding officers found the body and summoned homicide detectives to the scene. The man, who was estimated to be in his 50s, was pronounced dead at the scene.

By Matt Rocheleau, Globe Correspondents

Nicole Reis approached the Boston Marathon finish line in Copley Square holding the baton aloft as her father, John Odom, and other jovial spectators proudly cheered her on a few feet away from a sidewalk along Boylston Street. Much of the scene matched how it was supposed to have happened 2½ months ago, except most noticeably the time — about 12:45 a.m. Monday — and that Odom sat in a wheelchair. His leg was severly injured by one of two bombs that exploded near the finish line as he stood waiting to see his daughter who was stopped by race organizers before she could ever complete the race.

By Derek J. Anderson, Globe Correspondent

Two State Police troopers patrolling the Esplanade broke up an apparent sexual assault in the area of the Longfellow Bridge early this morning, according to the Suffolk District Attorney Daniel F. Conley’s office. The troopers arrested 49-year-old Joseph Barthel for indecent assault and battery, said Conley’s office. The victim, an adult female, was transported to a local hospital and was not seriously physically injured, said Jake Wark, a spokesman for Conley

By Matthew Higgins, Globe Correspondent

The missing Newton teenager authorities began searching for Saturday night was found safely in Boston on Sunday and returned home. Ana Lopez, 16, had been missing since June 26 at about 4:30 p.m., said police, and hadn’t been in contact with any friends or family members. On Saturday, police began a physical search of the Hammond Pond area of Newton based on location information from the last ping of her cell phone.

By Gal Tziperman Lotan, Globe Correspondent

One of two men shot on Harvard Street in Dorchester Saturday night was a customer in a liquor store, hit by an errant bullet, said Doug Rodman, whose wife’s family owns the store. The bullet that went through the window of Gigi’s Liquors, 144 Harvard St., pierced a customer’s arm, Rodman said. The two victims were taken to Boston Medical Center and are expected to live, police said in a statement. No arrests had been made as of early this afternoon.

By Haven Orecchio-Egresitz, Globe Correspondent

Two people were shot Saturday night at a liquor store in Dorchester, Boston police said. Authorities responded to Gigis Liquors at 144 Harvard Street around 10:30 p.m., according to Officer Katherine Shea. One person was shot in the store and the other just outside, she said. The sex, age and condition of the victims were not immediately available. The investigation is ongoing and police had no further details late Saturday night.

By Derek J. Anderson, Globe Correspondent

The distraught mother of missing 16-year-old Ana Lopez left a simple message with the media outside the Newton Police Department Saturday night: “We love her and we are concerned about her well-being.” Lopez has not been seen or heard from since about 4:30 p.m. June 26, said Newton Police Lieutenant Bruce Apotheker.

By Dan Adams, Globe Correspondent

A man wanted in connection with former football star Aaron Hernandez’s alleged slaying of Odin Lloyd will waive his right to a rendition hearing and be sent to Massachusetts “as soon as possible,” the man’s attorney said today. Ernest Wallace, 41, turned himself into police in Miramar, Fla. Friday after learning authorities had issued a warrant for his arrest, defense attorney David Meier said. He is being held without bond while he awaits rendition on charges of being an accessory after the fact to murder.

By Jeff Fish, Globe Correspondent

The body of a man in his 40s was recovered from the water at Winthrop Beach this afternoon, according to the Winthrop Fire Department. Firefighters received a call around 2 p.m. from residents near Faun Bar, in the area of Beacon Street and Winthrop Shore Drive, reporting a body floating by the shore, said Fire Captain Charles Flanagan. The victim has not been identified, and police are investigating.

By Wesley Lowery, Globe staff

Mourners spilled out of the front doors of an aged Mattapan church, where they gathered Saturday morning to remember a brother, son, friend, and a teammate. More than 275 people packed the green cushioned pews and the aisles of Church of the Holy Spirit attending the funeral service for Odin Lloyd, the 27-year-old Dorchester man whose body was found earlier this month in North Attleborough. Another 150 people listened in a nearby overflow room, while another hundred stood outside, unable to get a seat.

Two men were injured within minutes Friday night in unrelated shootings in Roxbury and Dorchester, police said. Superintendent William Evans said a man was shot in the upper body at about 8 p.m. on Fenno Street in Roxbury, near Walnut Avenue. He was taken to Boston Medical Center for treatment. Police arrested one unidentified suspect and recovered a gun near the shooting scene, but another man fled to a nearby apartment building and later escaped. Police said another male victim was shot in the leg on Edwin Street in Dorchester about 20 minutes before the Roxbury shooting. He was taken to the same hospital. Police said neither man’s injuries were considered life-threatening.

By Travis Andersen, Globe Staff

State public health officials have detected the first mosquito of the summer carrying the West Nile virus, which can cause ailments including joint aches and nausea when passed to humans, in the town of Whitman. The mosquito was collected Tuesday, and staff at the State Laboratory Institute in Jamaica Plain confirmed the infection Friday, said the Department of Public Health in a statement.

By Todd Feathers, Globe Correspondent

Two Lawrence men who allegedly robbed a TD Bank at gunpointThursday only to be caught 15 minutes later by police were arraigned today in Lawrence District Court, a prosecutor said. Not guilty pleas were entered on behalf of Juan Muniz, 33, and Pablo Ortiz, 37, said Carrie Kimball Monahan, a spokeswoman for the Essex County District Attorney’s office.

By Lauren Dezenski, Globe Correspondent

Storms have begun popping up in the western part of the state, with conditions ripe for strong to severe thunderstorms in the greater Boston area, but not in southeastern Massachusetts, the National Weather Service said this afternoon.

By Brian Ballou, Globe Staff

The disclosure by law enforcement officials that Aaron Hernandez is being investigated in connection with a deadly double shooting in Boston’s South End last year that claimed the lives of two Dorchester men and left another man wounded caused a flood of emotion for their families this week. On July 16, 2012, someone from a silver or gray SUV opened fire on a BMW sedan stopped at a traffic light at the corner of Shawmut Avenue and Herald Street, killing Daniel Abreu, 29, and Safiro Furtado, 28, according to Boston Police . Another passenger was wounded. Two other occupants fled the car unharmed.

By Shelley Murphy and Milton J. Valencia, Globe Staff

A disgraced former FBI supervisor told a US District Court jury today that he panicked in 1995 when federal prosecutors arrested Stephen “The Rifleman” Flemmi, out of fear that the member of the Winter Hill Gang would expose the FBI agent’s own crimes to law enforcement. “I was worried about everything surfacing,” said John Morris, a former supervisor of the organized crime unit at the Boston FBI office who retired that same year. “I certainly did not want my bad behavior known in any way, shape or form.”

By Travis Andersen, Wesley Lowery, Mark Arsenault, Meghan E. Irons and John R. Ellement, Globe Staff

Ernest Wallace, the third suspect in the murder of Odin L. Lloyd, walked into the police station in the southern Florida community of Miramar today where he peacefully surrendered to police. “He announced that he had a warrant and had seen himself on television and wanted to turn himself in,” said Officer Gil Bueno, a Miramar police spokesman.

By Todd Feathers, Globe Correspondent

Somebody shouted out a warning, and Viking Gustafson and her coworkers at the Marine Railways shipyard in Gloucester dove for cover as the swarm came buzzing out of a sheet of rain. Gustafson, epinephrine pen in hand, watched from a safe distance as 25,000 honey bees, moving as one, took over the shipyard Wednesday afternoon. The 50-foot long, 25-foot wide swarm covered a corner of the yard before coagulating on a piece of scaffolding into a single, basketball-sized mass.

By Meghan E. Irons, Globe Staff

One picture is of Odin L. Lloyd as a toddler gripping to his mother’s floral settee and staring into the camera like he’s discovered something marvelous — like walking. In another photograph he is a bigger, bulkier boy dressed in a black suit with a silver vest and smiling coolly with his mother and two sisters. There are other pictures, too, of Lloyd over his 27 years. Funeral services for the Dorchester man allegedly murdered by a former New England Patriot are set for Saturday.

By Wesley Lowery, Globe staff

Officials have located and recovered the silver Chrysler 300 with Rhode Island license plates that prosecutors were searching for in relation to the Odin L. Lloyd murder investigation, according to the Bristol, Conn., resident who spotted it and called it in. Also today, police in Florida arrested Ernest Wallace, who is accused of being an accessory after the fact to Lloyd’s June 17 murder.

By Lauren Dezenski, Globe Correspondent

Two Revere men are facing charges after allegedly stealing over $5,000 in copper wire from a dumpster outside a Wellesley municipal building, Wellesley police said. Sean Bussey, 44, and Mark Ferragamo, 43, allegedly broke into the Wellesley Municipal Light Plant’s secure yard the weekend of June 22 and took the wire. The two men have pleaded not guilty to all charges.

By Travis Andersen, Globe Staff

Authorities are searching for a third suspect in connection to the slaying of 27-year-old Odin L. Lloyd, calling Ernest Wallace, 41, “armed and dangerous.” In a statement, the Bristol District Attorney’s Office said that Wallace is wanted on a charge of accessory after the murder of Lloyd, a 27-year-old Dorchester man who was allegedly shot to death by former Patriots player Aaron Hernandez on June 17. Wallace has active felony warrants in Massachusetts, police said.

By David Abel, Martin Finucane and John R. Ellement, Globe Staff

A federal grand jury today handed up a sweeping indictment of Boston Marathon bombings suspect Dzhokhar A. Tsarnaev, charging him with using weapons of mass destruction and killing four people. The 30-count indictment alleges that Tsarnaev had been inspired by Al Qaeda publications and left a confession in the boat where he was captured in a Watertown back yard.

By Maria Cramer, Globe Staff

Former New England Patriots player Aaron Hernandez, already facing charges in a murder last week in North Attleborough, is also being investigated in connection with a July 2012 double murder in Boston, according to two law enforcement officials briefed on the investigation. Investigators believe the slayings happened after a fight broke out at Cure, a club in the South End, between two men and a group that included Hernandez.

By Javier Panzar, Wesley Lowery, Travis Andersen and John R. Ellement, Globe Correspondent and Globe Staff

Police on Wednesday found .45-caliber bullets in a condo rented by former New England Patriots star Aaron Hernandez and in a car linked to him, the same caliber ammunition Hernandez allegedly used to shoot and kill Odin L. Lloyd in a North Attleborough industrial park on June 17, a prosecutor said today. The new disclosure about a possible forensic link between Hernandez and the murder of Lloyd, a 27-year-old Dorchester man, was made in Bristol Superior Court, where attorneys for Hernandez asked Judge Renee P. Dupuis to allow him to be freed on bail while he fights a first-degree murder charge.

By Lauren Dezenski, Globe Correspondent

A cluster of rainstorms is rolling into the Boston area, kicking off showers and thunderstorms expected to last through the rest of the workweek. The National Weather Service has issued a flash flood watch as a low pressure system is expected to stall over the region. The rainfall is expected to be heaviest in areas south of the Massachusetts Turnpike.

By Milton Valencia, Globe Staff

A retired Miami police sergeant testified in federal court today that he found the wallet and license of businessman and murder victim John B. Callahan in a Cuban neighborhood of Miami, corroborating testimony that James “Whitey” Bulger wanted to make it look like Callahan was killed by Cubans in a deal that had gone bad.

By Lauren Dezenski, Globe Correspondent

An early morning four-alarm fire has left a Somerville condominium uninhabitable, displacing 23 residents, according to Somerville firefighters and the American Red Cross. The fire was discovered around 5 a.m. at 106 Walnut St., which was built in 1920 and currently comprises six condo units, according to Somerville assessment records. The fire appears to have started in the basement, Somerville Fire Chief Kevin Kelleher said. It took firefighters about two hours to knock down the fire.

By Martine Powers, Globe Staff

State legislators have voted to approve a compromise transportation funding plan that will raise taxes to fund investment in the state’s transportation department, but Governor Deval Patrick said the amount raised by the bill is not enough. After the house passed the spending plan with a 105-47 vote, Patrick issued a statement saying that the bill will not meet the state’s transportation needs.

By Shelley Murphy and Milton J. Valencia, Globe Staff

James “Whitey” Bulger glared at a disgraced former FBI official who was testifying against him and told him, “You’re a [expletive] liar,” a federal prosecutor said today at the notorious gangster’s trial. Assistant US Attorney Brian T. Kelly said Bulger shouldn’t be allowed to intimidate John Morris as he once threatened 15-year-old boys in South Boston. Speaking after jurors had left the courtroom, he asked US District Judge Denise J. Casper to admonish Bulger.

By John R. Ellement, Globe Staff

Boston police have arrested a man and charged him with killing a 33-year-old woman who was found dead inside her home at East Fourth Street in South Boston Wednesday night. Martin Jiminez is to be arraigned today in South Boston Municipal Court, according to Suffolk District Attorney Daniel F. Conley’s office. The woman’s name is currently being withheld pending notification of next of kin.

By Meghan Irons, Globe Staff

A member of Odin Lloyd’s family recalled the slain 27-year-old as someone with a “grin that you couldn’t miss” as word spread this afternoon that former New England Patriots player Aaron Hernandez had been charged in the murder. “I would say to him stay out of trouble, and he would say, ‘Always, auntie,’” said the woman, who is Lloyd’s mother’s cousin. She would not disclose her name.

By Lauren Dezenski, Globe Correspondent

Two Registry of Motor Vehicle officials and a service station owner pleaded not guilty to charges of extortion and fraud after allegedly scheming to create a “black market” for motor vehicle safety inspection licenses, United States Attorney Carmen M Ortiz and Boston FBI Special Agent Richard DesLauriers said in a statement today.

By Lauren Dezenski, Colin A. Young, Wesley Lowery and John R. Ellement, Globe Correspondents and Globe Staff

Former New England Patriots player Aaron Hernandez executed his acquaintance Odin L. Lloyd because Hernandez was upset that Lloyd had spoken at a Boston nightclub on June 14 with people Hernandez “had troubles with,” a prosecutor alleged today. In a dramatic hearing in Attleboro District Court, a Bristol County prosecutor said surveillance videos in Boston, in North Attlebrough, and even in Hernandez’s own home linked him to the slaying several days later of Lloyd.

By Todd Feathers, Globe Correspondent

The Boston City Council today unanimously approved a $2.6 billion budget for the next fiscal year as well as nearly $1 billion for the city’s public schools. The funding marks a 5.2 percent increase over the current fiscal year 2013 budget, according to Mayor Thomas M. Menino’s office. The 12-member council also unanimously approved $937.4 million for the Boston Public Schools in fiscal year 2014 and $1.8 billion over five years for capital projects, Menino’s office said.

By Alyssa A. Botelho and John R. Ellement, Globe Correspondent and Globe Staff

At the downtown Boston offices of Gay & Lesbian Advocates & Defenders, Lee Swislow said she and others at the civil rights group are both elated and in disbelief that the US Supreme Court has embraced same-sex marriage. “We are feeling a great joy tinged with a touch of disbelief that this day finally came,’’ said Swislow, the executive director of the organization, which has spent more than 20 years seeking equal rights for same-sex couples in courtrooms across the country.

By Todd Feathers, Globe Correspondent

A Lexington man has pleaded guilty to indecently assaulting a young girl at the Arlington karate school where he coached her, prosecutors said. Middlesex Superior Court Judge Kathe Tuttman sentenced 52-year-old Thomas Donahue to2½ years in jail followed by three years of probation, according to Middlesex District Attorney Marian T. Ryan’s office.

By Jasper Craven, Globe Correspondent

We may be out of the stifling heat wave that gripped much of the state earlier in the week, but don’t expect the humid weather to disappear anytime soon. Temperatures today are dipping into the mid- to upper 80s with showers and thunderstorms peppering communities throughout the state, according to the National Weather Service.

By Travis Andersen and Alyssa Botelho, Globe Staff and Globe Correspondent

Prominent Boston criminal defense lawyer James L. Sultan visited the home of New England Patriots tight end Aaron Hernandez this afternoon, amid the ongoing homicide investigation that has embroiled the star player for more than a week. Sultan, who has represented a number of high-profile clients, including a former Citibank executive convicted of murdering his girlfriend in 2004 on Nantucket, for whom the lawyer won a new trial, entered Hernandez’s home with another man shortly after 3 p.m.

By Brian Ballou, Globe Staff

With no arrests yet in the triple homicide at a house party in Dorchester early Saturday, the family and friends of one of the victims, Felix Garcia, spoke about how he had taken on new responsibility recently and dreamed of a stable adulthood. Garcia’s sisters, Michelle, 14, and Bryana, 17, said was always encouraging them to do their best.

By Todd Feathers, Globe Correspondent

A Southington, Conn., man who allegedly stole a woman’s clutch wallet in Dorchester left his birth certificate and a letter from his mother behind at the scene of the crime, making him an easy target for police, the Boston police said today. Officers responded to the Harbor Middle School schoolyard at 11:54 p.m. Monday and spoke with a woman who said a man had followed her into the yard and then snatched her wallet, which contained her ID, Charlie Card, and $40 in cash, according to police.

By Lauren Dezenski, Globe Correspondent

Who’s that third person on the ballot for the Massachusetts special election for US Senate? Woburn resident Richard Heos, a candidate for the 12 Visions Party. Heos said he’s pro-business and is using his candidacy to advance his party’s status. Heos described the 12 Visions Party as a nonpolitical party that seeks to devolve power to local law enforcement and end entitlement programs and taxation.

By Todd Feathers, Globe Correspondent

Amtrak customers traveling between Boston and New Haven, Conn., should expect delays of up to two hours due to a disabled maintenance train, a railroad spokesman said. A maintenance train became disabled around 12:15 p.m., blocking tracks in both directions, while it was replacing concrete ties, spokesman Cliff Cole said.

By Lauren Dezenski and Todd Feathers, Globe Correspondents

An explosion likely caused by a buildup of gas killed a 55-year-old man and destroyed his Yarmouth, Maine, condominium this morning, a state fire official said. The man has not been identified. He was the only person injured in the explosion, said Sergeant Joel Davis of the Maine fire marshal’s office.